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Soil microbial ecology through the lens of metatranscriptomics

SOIL ECOLOGY LETTERS 2024年第3期6卷 230217-230217页

作者： Peng, Jingjing Zhou, Xi Rensing, Christopher Liesack, Werner zhu, yong-guan China Agr Univ Natl Acad Agr Green Dev Coll Resources & Environm Sci Key Lab Plant Soil InteractMinist EducState Key Beijing 100193 Peoples R China Fujian Agr & Forestry Univ Inst Environm Microbiol Coll Resources & Environm Fuzhou 350002 Peoples R China Max Planck Inst Terr Microbiol D-35043 Marburg Germany Chinese Acad Sci Res Ctr Ecoenvironm Sci State Key Lab Urban & Reg Ecol Beijing 100085 Peoples R China Chinese Acad Sci Key Lab Urban Environm & Hlth Inst Urban Environm Xiamen 361021 Peoples R China

Metatranscriptomics uncovers the dynamic expression of functional genes in soil environments, providing insights into the intricate metabolic activities within microbial *** enrichment from soil samples remains a formidable challenge due to the presence of inhibitory compounds, low RNA yields, and sample *** metatranscriptomics unravels the expression levels of genes involved in the real-time molecular dialogues between plants and rhizobionts, uncovering the dynamics of nutrient exchange, symbiotic interactions, and plant-microbe *** unlocks the active expression of the soil resistome, elucidating the mechanisms of resistance dissemination under anthropogenic *** provides comprehensive data regarding the identification, quantification, and evolutionary history of RNA viruses. 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 conditions. The double-RNA approach involves the simultaneous analysis of rRNA and mRNA, also termed structural and functional metatranscriptomics. By contrast, mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles, but requires either deep sequencing or effective rRNA depletion. In 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 metatranscriptomics. In 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 viromes. Our review provides a framework that will help to design advanced metatranscr

关键词： metatranscriptomics mRNA MAGs rhizobiont resistome virome RIBOSOMAL-RNA READ ALIGNMENT MESSENGER-RNA IDENTIFICATION DEGRADATION SEQUENCE ROOT SEQ

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Prevention and control strategies for antibiotic resistance: from species to community level

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SOIL ECOLOGY LETTERS 2024年第3期6卷 230222-230222页

作者： Wang, Yan-Zi Li, Hu Chen, Qing-Lin Pan, Ting zhu, yong-guan Springael, Dirk Su, Jian-Qiang Chinese Acad Sci Inst Urban Environm Key Lab Urban Environm & Hlth Ningbo Observat & Res Stn Xiamen 361021 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Chinese Acad Sci Res Ctr Ecoenvironm Sci State Key Lab Urban & Reg Ecol Beijing 100085 Peoples R China Katholieke Univ Leuven Div Soil & Water Management Box 2459Kasteelpark Arenberg 20 B-3001 Heverlee Belgium

ARGs and ARB in typical environments which exposed to antibiotics are ***- and photosensitizer-related technology can clear specific ARGs or ***-Cas- and phage-related technology can eliminate particular ARGs or *** combination can be used to eliminate microbial ***-specific technology can eradicate most types of ARGs or ARB in one *** resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment pose serious threats to environmental security and public health. There is an urgent need for methods to specifically and effectively control environmental pollution or pathogen infection associated with ARGs and ARB. This review aims to provide an overview of methods abating the prevalence and spread of ARGs and ARB from species to community level. At the species level, species-specific technologies, such as nanoparticle-, photosensitizer-, CRISPR-Cas-, and phage-related technology can be utilized to clear a particular class of ARGs or ARB, and in combination with low-dose antibiotics, a higher removal efficiency can be achieved. Moreover, the combination of antibiotics can be used to reverse microbial resistance and treat recurrent antibiotic resistant pathogen infections. At the community level, community-specific strategies, such as biochar, hyperthermophilic compost, and fecal microbiota transplantation can eradicate most types of ARGs or ARB in one shot, reducing the probability of resistance development. Though some progress has been made to eliminate ARGs and ARB in disease treatment or decontamination scenarios, further research is still needed to elucidate their mechanisms of action and scopes of application, and efforts should be made to explore novel strategies to counter the prevalence of antibiotic resistance.

关键词： antibiotic resistance genes antibiotic resistant bacteria treatment strategy disinfection FECAL MICROBIOTA TRANSPLANTATION PHOTODYNAMIC THERAPY WATER-TREATMENT POLYVALENT BACTERIOPHAGE COMBINATION THERAPIES MOLECULAR-MECHANISMS PATHOGENIC BACTERIA HORIZONTAL TRANSFER BIOCHAR AMENDMENT ESCHERICHIA-COLI

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菌根真菌在陆地生态系统碳循环中的作用

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植物生态学报 2024年第1期48卷 1-20页

作者：陈保冬付伟伍松林朱永官中国科学院生态环境研究中心城市与区域生态国家重点实验室中国科学院大学

在陆地生态系统中,土壤、植被与大气之间有着可观的碳交换通量,陆地生态系统碳循环也和全球气候变化密切关联。菌根真菌可与绝大多数陆地植物建立菌根共生关系,通过矿质养分-碳交换连接起生态系统地上与地下部分,深度参与和影响陆地生... 详细信息

在陆地生态系统中,土壤、植被与大气之间有着可观的碳交换通量,陆地生态系统碳循环也和全球气候变化密切关联。菌根真菌可与绝大多数陆地植物建立菌根共生关系,通过矿质养分-碳交换连接起生态系统地上与地下部分,深度参与和影响陆地生态系统的碳循环过程。该文从碳的输入,土壤有机质的形成、稳定和分解等4个关键环节分别论述了菌根真菌在陆地生态系统碳循环中的作用。研究表明,菌根真菌在陆地生态系统碳的输入过程中扮演关键角色,其通过改善植物矿质营养,参与植物逆境响应,影响植物的光合作用强度,以及调控植物多样性与生产力之间的关系等多种途径,维持或提高植被初级生产力;大气中的CO2被植物固定后,一部分碳经由菌丝网络输送到土壤中,随后经微生物的分解和转化,与矿物结合或被团聚体包裹而被稳定在土壤中;同时,菌根真菌通过影响根际激发效应和菌丝际生物化学过程,如分泌特定胞外酶,与菌丝际微生物互作,驱动芬顿反应,以及与腐生微生物竞争等,调控土壤有机质的分解和转化过程。考虑到菌根真菌对环境和气候变化的敏感性,该文还探讨了全球变化因子对菌根真菌介导的碳循环过程的影响。最后,该文对未来研究方向进行了展望,并提出以下建议:依托联网研究,全面解析菌根真菌参与陆地生态系统碳循环的机理过程及其环境依赖性;加强定量研究,将菌根真菌的作用纳入生态系统碳循环模型;构建菌根应用技术体系,推进菌根真菌的生态和农业应用,提升陆地生态系统“碳汇”功能,为实现国家碳中和目标和应对气候变化提供可选择的技术方案。

关键词：陆地生态系统碳循环全球变化丛枝菌根真菌外生菌根真菌土壤有机质

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Arsenate and phosphate interaction in Saccharomyces cerevisiae

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Journal of Environmental Sciences 2006年第1期18卷 96-100页

作者： GENG Chun-nu zhu yong-guan Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China Shanghai Academy of Environmental Sciences Shanghai 200233 China

In the present study, arsenate（As（V）） and phosphate（P（V）） interactions were investigated in growth, uptake and RNA content in yeast（Saccharomyces cerevisiae）. Yeast grew slowly with As（V） concentrations increasing in the medium. However, the maximal population density was almost the same among different As（V） treatments. It was in the late log phase that yeast growth was aug- mented by low As（V）, which was maybe due to the fact that methionine metabolism was stressed by vitamin B6 deprivation, so As（V） treatments did not affect maximal population density. However, with P （V） concentrations increasing, the maximal population density increased. Therefore, the maximal population density was determined by P （V） concentrations in the medium but not by As （V） concentrations in the medium. Ycflp（a tonoplast transpor） transports As（GS）3 into the vacuole, but arsenic（As） remaining in the thalli was 1.27% with As（V） exposure for 60 h, from which it can be speculated that the percentage of As transported into vacuole should be lower than 1.27%. However, the percentage of As pumped out of cell was 71.49% with As （V） exposure for 68 h. Although two pathways （extrusion and sequestration） were involved in As detoxification in yeast, the extrusion pathway played a major role in As detoxification. RNA content was the highest in the early-log phase and was reduced by As（V）.

关键词： yeast maximal population density arsenic essentiality arsenic speciation

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Risk assessment of heavy metal contaminated soil in the vicinity of a lead/zinc mine

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Journal of Environmental Sciences 2005年第6期17卷 881-885页

作者： LI Jing XIE Zheng-miao zhu yong-guan Ravi Naidu Institute for Soil and Water Resources and Environment Zhejiang University Hangzhou 310029 China Research Centre for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China Centre for Environmental Risk Assessment and Remediation University of South Australia Mawson Lakes SA 5095 Australia

Heavy metal contamination of soils through anthropogenic activities is a widespread and serious problem confronting scientists and regulators throughout the world. In this study we investigated the distribution, chemical species and availability of lead, zinc, cadmium and copper in nine surface（0 to 20 cm） soils from near an abandoned lead/zinc mine tailings located in Shaoxing, Zhejiang, China. Total heavy metal contents ranged from 5271 to 16369 mg/kg for Pb, 387 to 1221 mg/kg for Zn, 3.0 to 9.3 mg/kg for Cd and 65 to 206 mg/kg for Cu. In general, all heavy metals exceeded China National Standards for Soil Environmental Quality of Heavy Metals by a factor of 3-65 times. Comparison of the heavy metal concentrations（Pb, Zn, Cd and Cu） with clay content revealed a strongly significant relationship while significant relationship（ P 〈 0.001 ） was also obtained between Cd ＋ Zn and Pb ＋ Cu. Solid phase speciation of the soils using Tessier procedure showed that the heavy metals were distributed in the order： residual 〉〉 organically complexed-Fe-Mn oxides occluded 〉 carbonate bound 〉 exchangeable 〉 water soluble. In the organic matter fraction, the ratio of Pb（29.1% ） to its total concentration in the soils was higher than those of Zn（4.70% ）, Cd（3.16% ） and Cu（9.50% ）. The percentages of the water soluble and the exchangeable fractions of Pb（1.80% ） and Cd（2.74% ） were markedly greater than those of Zn（0.10% ） and Cu（0.15% ）, suggesting that Pb and Cd are relatively more mobile and hence more toxic in the contaminated soils. Strongly significant relationships between H20-Pb, H20-Zn and H20-Cu, strong positive correlations between H20-Pb, H20-Zn, H20-Cu and organic matter in soil were found. The content of H20-Pb, H20-Zn, H20-Cu was negatively correlated with pH values. The similar negative relationships between pH values and exchangeable heavy metals were also recorded. It is suggested that increasing soil pH or liming the soil could decrease bioavailability of heavy met

关键词： fractionation heavy metal mining tailings risk assessment soil pollution

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Ecological effects of crude oil residues on the functional diversity of soil microorganisms in three weed rhizospheres

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Journal of Environmental Sciences 2006年第6期18卷 1101-1106页

作者： ZHANG Qian-ru ZHOU Qi-xing REN Li-ping zhu yong-guan SUN Shu-lan Key Laboratory of Terrestrial Ecological Process Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 China Graduate School of Chinese Academy of Sciences Beijing 100039 China College of Environmental Science and Engineering Nankai University Tianjin 300071 China Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China Kyushu University Fukuoka 8128582 Japan

Ecological effects of crude oil residues on weed rhizospheres are still vague. The quantitative and diversity changes and metabolic responses of soil-bacterial communities in common dandelion （Taraxacum officinale）, jerusalem artichoke （Silphiurn perfoliatum L.） and evening primrose （A colypha australis L.） rhizospheric soils were thus examined using the method of carbon source utilization. The results indicated that there were various toxic effects of crude oil residues on the growth and reproduction of soil bacteria, but the weed rhizospheres could mitigate the toxic effects. Total heterotrophic counting colony-forming units （CFUs） in the rhizospheric soils were significantly higher than those in the non-rhizospheric soils. The culturable soil-bacterial CFUs in the jerusalem artichoke （S. perfoliatum） rhizosphere polluted with 0.50 kg/pot of crude oil residues were almost twice as much as those with 0.25 kg/pot and without the addition of crude oil residues. The addition of crude oil residues increased the difference in substrate evenness, substrate richness, and substrate diversity between non-rhizospheric and rhizospheric soils of T. officinale and A. australis, but there was no significant （p〉0.05） difference in the Shannon＇s diversity index between non-rhizospheric and rhizospheric soils of S. perfoliatum. The rhizospheric response of weed species to crude oil residues suggested that S. perfoliatum may be a potential weed species for the effective plant-microorganism bioremediation of contaminated soils by crude oil residues.

关键词： ecological effect weed rhizosphere crude oil residue soil microorganism functional diversity

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Relationships Between Agronomic and Environmental Soil Test Phosphorus in Three Typical Cultivated Soils in China

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Pedosphere 2008年第6期18卷 795-800页

作者： WANG Xin-Min JIE Xiao-Lei zhu yong-guan HOU Yan-Lin ZHANG Tie-Quan Zhengzhou College of Animal Husbandry Engineering Zhengzhou Henan 450011 （China） Department of Soil Environmental Science ResearchCenter for Eco-Environmental Sciences Chinese Academy of Sci-ences Beijing 100085 （China） Greenhouse and Processing Crops Research Center Agriculture ~z Agri-Food Canada Harrow Ontario NOR 1 G （Canada）

A study was conducted to determine the relationships between agronomic soil test P and environmental soil test P in three soils predominately distributing in three typical agricultural production areas of China. Soil P was analyzed using Bray-1 （BP）, Olsen （OP）, and Mehlich-3 （MP） methods as agronomic tests, and using Fe-oxide impregnated filter paper （FeP）, anion-exchange resin membrane （RP）, and water （WP） as environmental tests. There were linear relationships between soil P extractable with all the tests evaluated. The regression coefficients, R^2, ranged from 0.8164 to 0.9409 between each two of the agronomic soil test P, and ranged from 0.4702 to 0.8990 between each two of the environmental soil test P, when the three soils were considered separately. When soil test P was analyzed across all the three soils, the highest regression R^2 was found between OP and MP （0.7940） amongst agronomic soil test P, and between FeP and RP amongst environmental soil test P （0.8842）. While all of the three agronomic soil test P was linearly related to each of the environmental soil test P across the three soils, strongest relationships were found between OP and environmental soil test P. Agronomic OP may be adopted as an analytical tool for environmental prediction of soil P.

关键词： environment phosphorus testing methods

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A survey of arsenic and other heavy metals in vegetation from markets or mine tailings

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Journal of Environmental Sciences 2006年第2期18卷 287-291页

作者： LIU Wen-ju Kim Kyoung-woong zhu yong-guan LEE Sang-woo CHANG Pei-chun Kwak Ji-hyun Department of Environmental Science and Engineering Gwangju Institute of Science and Technology （GIST） Gwangju 500-712 Korea Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China College of Natural Resources and Environment Hebei Agricultural University Baoding 071001 China

This research includes two investigations. The first one is a market basket survey of the levels of arsenic （As） and trace elements in bracken fern （Pteridium aquilinum） originated from three countries： South Korea, China and North Korea. The results showed that the mean As concentrations in stems of samples were significantly higher than those in leaves. As concentrations in all samples did not exceed food safety limits for vegetables. Generally, concentrations of Fe, Mn, Cu and Zn in leaves were higher than those in stems. The second investigation is a survey on the levels of As and other heavy metals in vegetation in the vicinity of Myoungbong mine tailings. The results demonstrated that As, Pb and Cu concentrations and bioaccumulation factors （BCF） in seedlings of the fern（A splenium achilleifolium） were the highest, whereas Marsh horsetail（Equisetum polustre） accumulated the highest levels of Zn. Concentrations of As, Pb, Zn and Cu in vegetable-cress （Lepidium sativum） and the edible herb-aromatic madder （Elasholtzia splendens） were higher than food safety limits. Therefore, a risk assessment of As and other heavy metals in vegetables and herbs on local human health should be conducted in the future.

关键词： arsenic heavy metals ferns bioaccumulation factors

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Collembolans maintain a core microbiome responding to diverse soil ecosystems

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Soil Ecology Letters 2024年第1期6卷 33-46页

作者： Zhe-Lun Liu Dong zhu Yi-Fei Wang yong-guan zhu Min Qiao State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China Key Lab of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China

The unique gut habitat led to a core intestinal micro-biome in diverse soil *** collembolan guts may help eliminate soil ***-selection carried more weight on community assembly of gut *** invertebrates are widely distributed in the ecosystem and are essential for soil ecological ***-brate gut microbiome plays an important role in host health and has been considered as a hidden microbial ***,little is known about how gut microbiome in soil invertebrates respond to diverse soil *** on a laboratory microcosm experiment,we characterized the assembling of microbiome of soil collembolans(Folsomia candida)from six representative regions of the soil ecosystem which they *** showed that collembolan gut microbial communities differed significantly from their surrounding soil microbial communities.A dominant core gut microbiome was identified in gut *** analyses indicated that deterministic process dominated in the community assembly of collembolan gut *** results further demonstrate a dominant contribution of host selection in shaping gut *** is also worthy to mention that pathogens,such as common agricultural phytopathogenic fungi Fusarium,were involved in core microbiome,indicating that collembolans could act as vectors of *** results unravelled the existence of gut core microbiome of collembolans in soil ecosystems and provided new insights for under-standing the crucial role of gut microbiome of soil fauna in maintaining microbial biodiversity and stability of soil ecosystems.

关键词： gut microbiome collembolan core microbiome community assembly

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Harnessing the holobiont to alleviate the stress of aluminum toxicity to rice

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Soil Ecology Letters 2024年第1期6卷 7-9页

作者： Hong-Zhe Li yong-guan zhu Key Lab of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China Fujian Key Laboratory of Watershed Ecology Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China Research Center for Eco-Environmental Sciences Chinese Academy of SciencesBeiing 100085China

Plant microbiome(including the microbiomes in the rhizosphere,phyllosphere,and endosphere)has been hailed as the second genome of the host,and plays a critical role in the health and fitness of the *** to clinical medicine,microbiome transplant has been suggested to improve ecosystem restoration and crop production in degraded environment(Jurburg et al.,2022).This concept aligns with recent findings that emphasize the significant impact of soil and plant-associated microbiomes in agricultural productivity and the health of host plants(Wubs et al.,2016;Carthey et al.,2020;Mazza Rodrigues and Melotto,2023).

关键词： finding Harness soil

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