土壤病毒的研究进展与挑战

病毒是由蛋白质和核酸组成的结构简单的非细胞型生物实体,全球病毒数量估算为4.80?1031,远高于具有细胞型结构的生物数量。土壤是病毒重要的储藏库,土壤中病毒主要以侵染原核生物的噬菌体为主,其数量与寄主细胞数目和土壤理化指标密切相关。虽然学术界已意识到土壤病毒在调控微生物群落结构组成、影响土壤元素循环利用、促进生物进化、以及影响动植物病害乃至人类健康等方面可能起到重要的作用,但由于受到土壤病毒颗粒的吸附性、土壤异质性,以及研究手段和分析平台的制约,我们对土壤病毒的认知和重视程度远落后于流动的海洋等水体环境。土壤病毒宏基因组中大量的基因序列无法判断其来源及功能,被划分为未知基因,所以病毒也被喻为生物“暗物质”和最大的未知基因宝库。本文在简要介绍了病毒的形态,在土壤中数量、存在形式和多样性的基础上,着重介绍了利用分子标记基因、RAPD和宏病毒组研究技术解析土壤病毒多样性的方法及其局限性,阐述土壤病毒已证实和潜在生态功能。最后,文章提出未来土壤病毒研究应加强的研究方向,强调土壤病毒与土壤微生物耦合研究在揭示土壤生态功能研究中的重要性。     

一个东北农田黑土样品宏病毒组的初步分析

病毒在地球上无处不在,几乎能感染任何生物,包括动物、植物、真菌以及细菌等,因而在生物地球化学元素和能量的循环过程中发挥重要作用。了解土壤病毒基因信息有助于我们深入理解病毒在生态系统中所扮演的角色。本研究选取一个东北农田黑土样品中的病毒为研究对象,基于病毒宏基因组测序技术获得土壤病毒基因序列,并利用生物信息分析方法揭示土壤病毒多样性。同时,结合个性化分析宏病毒组基因序列、进行功能基因分析、宿主预测和单病毒基因组组装和注释。研究发现该农田土壤检测到的病毒主要归属于有尾噬菌体目（Caudovirales,59.38%）和疱疹病毒目（Herpesvirales,2.56%）等2个病毒目中的29个病毒科,其中以长尾噬菌体科（Siphoviridae）、微小噬菌体科（Microviridae）的病毒数量最多,分别占44.48%和20.53%。基因功能分析表明土壤病毒可能参与土壤中的酶催化、生物代谢（如氮化合物代谢、分解代谢、多生物代谢、细胞代谢、初级代谢、含碱基小分子代谢以及有机物代谢等）等过程。宿主预测分析揭示检测到的病毒宿主分属5个菌门中的35个菌属。本研究结果丰富了土壤病毒的基因数据库,为土壤病毒分离提供参考,并为进一步理解土壤病毒生态学意义提供数据支撑。     

土壤病毒的研究进展与挑战

病毒是由蛋白质和核酸组成的结构简单的非细胞型生物实体,全球病毒数量估算为4.8010~(31),远高于具有细胞型结构的生物数量。土壤是病毒重要的储藏库,土壤中病毒主要以侵染原核生物的噬菌体为主,其数量与寄主细胞数目和土壤理化指标密切相关。虽然学术界已意识到土壤病毒在调控微生物群落结构组成、影响土壤元素循环利用、促进生物进化、以及影响动植物病害,乃至人类健康等方面可能起到重要的作用,但由于受到土壤病毒颗粒的吸附性、土壤异质性,以及研究手段和分析平台的制约,我们对土壤病毒的认知和重视程度远落后于流动的海洋等水体环境。土壤病毒宏基因组中大量的基因序列无法判断其来源及功能,被划分为未知基因,所以病毒也被喻为生物“暗物质”和最大的未知基因宝库。本文在简要介绍了病毒的形态,在土壤中数量、存在形式和多样性的基础上,着重介绍了利用分子标记基因、RAPD和宏病毒组研究技术解析土壤病毒多样性的方法及其局限性,阐述土壤病毒已证实和潜在生态功能。最后,文章提出未来土壤病毒研究应加强的研究方向,强调土壤病毒与土壤微生物耦合研究在揭示土壤生态功能研究中的重要性。     

温室黄瓜连作土壤真菌多样性变化分析

以温室黄瓜连作1、3、5和7年的根际土壤为研究对象,利用Illumina MiSeq高通量测序技术分析土壤真菌ITS1区域土壤微生物群落结构和多样性的变化,利用FUNGuild对菌群功能进行预测,同时测定不同连作年限土壤的理化性质和相关酶活性变化.结果表明:不同连作年限土壤真菌在门水平上的群落组成变化明显,子囊菌门在连...     

病毒在不同环境介质中去向研究进展

来自污水污泥等源头的病毒进入土壤和水环境后对人畜健康构成威胁,因而阐明病毒在不同环境中的去向是建立安全、高效病毒防治技术的基础.本文在已有研究的基础上,综述了病毒在水体、土壤中的去向,及病毒去除材料的去除效率和机制;明确了气-水界面、本土微生物、有机质含量及其组成等因素对病毒去向有显著影响;比较分析了基于高吸附性和铁铝氧化物致死性的活性炭和富铁铝材料等的病毒去除效率.最后从研究介质选择、病毒去除材料的潜在应用前景、及本土微生物组成对病毒去向影响角度提出了需进一步研究的一些建议.     

不同茬口和施氮水平对南瓜根际细菌碳分解潜力的影响

为探明根际细菌群落多样性及有机碳分解功能基因对耕作措施的响应特征,以收获小麦和西瓜后种植的南瓜根际土壤为研究对象,以两种施氮水平(纯氮施入量分别为1.0、2.0 g/kg)为处理,结合高通量测序和PICRUSt功能预测解析不同茬口和施氮水平下南瓜根际细菌群落结构和参与有机碳分解代谢细菌的关键功能基因丰度的差异.结果表明...     

大规模板栗疫病菌cDNA文库的特征和冗余序列的排除

低毒病毒/板栗疫病菌是一个研究病毒宿主相互作用的优良的实验系统.为了更好的了解病毒与宿主相互作用的机制,我们建立了一个野生型无病毒板栗疫病菌菌株EP155和受低毒病毒感染的菌株EP713的cDNA混和文库,以进行表达序列标签（EST）测定.对543个克隆的外源片段的分析表明,该文库克隆中含外源片段的比例为89.8%;通过小规模测序,发现空质粒与小片段克隆占测序总数的10.1%;表达丰度最高的4个克隆出现次数的总和占测序总数的9.6%.通过设计引物进行PCR和原位杂交,对cDNA文库2万多个克隆进行了筛选,共筛除了占总数19.7%的空质粒与小克隆和5.5%的高丰度克隆,为高效率的大规模EST测序准备了条件.     

土壤宏基因组学研究方法与进展

土壤微生物驱动着土壤中的物质循环和养分转化。在土壤学的研究中,长期将土壤作为一个黑箱系统来对待,对其中的生物组成及其参与的生化过程知之甚少。土壤中绝大部分微生物目前尚难以分离培养,因此基于传统的培养方法对于认识土壤微生物群落组成和功能有其局限性。宏基因组学直接从环境样品中提取全部微生物的DNA,或通过测序探究环境中微生物的群落结构和功能(序列驱动),或构建宏基因组文库,筛选新的基因或生物活性物质(功能驱动),克服了传统培养方法的缺陷,极大地丰富了对土壤微生物多样性及其功能的认知。本文在综述土壤宏基因组学研究基本流程的基础上,重点介绍了日益重要的第二代测序平台在土壤宏基因组学研究中的应用及其产生的海量数据的分析处理方法,并简要探讨了宏基因组学在土壤微生物生态学中的应用。最后,作者建议在国家层面上展开相关土壤宏基因组学研究,调查微生物群落及其变化,为生物资源开发、农业生产和环境保护作出应有的贡献。     

转Bt基因棉花根际细菌与古菌群落结构分析

在一年内棉花的四个生长时期（苗期,蕾期,花铃期,吐絮期）分别采集转Bt基因抗虫棉GK12和非转基因亲本棉花泗棉3号根际土壤,以及未种植棉花的背景土壤,利用末端标记限制性片段长度多态性（T-RFLP）分析技术,分析三种土壤中细菌和古菌的16S rRNA基因片段多态性,结合克隆文库建立和测序,研究了土壤中细菌和古菌群落结构的变化.结果表明：在棉花生长的各个时期,背景土壤中细菌群落结构发生了明显的变化,生物多样性指数明显降低,古菌群落结构也有一定的变化,说明季节性变化对土壤中微生物群落产生了明显的影响.与背景土壤相比,棉花种植后根际土壤中细菌和古菌群落发生显著的变化.转基因棉花与非转基因棉花相比,根际土壤细菌和古菌的种类和种群大小的分布也发生了明显的改变.克隆文库和测序结果表明土壤中主体微生物为目前未培养的、功能特性未知的细菌和古菌,转基因棉花种植对这些细菌和古菌影响的原因、环境危害和生态风险目前尚不清楚.与古菌群落相比,棉花种植对细菌群落结构的影响较小.     

生物质炭对连作参地土壤肥力及微生物特性的影响

为分析生物质炭用于老参地土壤修复的可行性,本研究采用Biolog、高通量测序等技术研究了3种生物质炭对连作参地人参品质、土壤肥力、微生物群落结构与功能多样性变化的影响。结果显示,增施不同生物质炭均有助于两年生重茬人参生物量及总皂苷含量的积累。结合生物质炭对土壤性质的影响研究结果发现,不同生物质炭对土壤有效磷、有机碳含量具有稳定的提升效果,增幅分别为47.04%~237.73%、8.09%~38.71%。增施生物质炭促进了土壤微生物的代谢活性,增加了土壤对聚合物类、酚酸类、氨基酸类、羧酸类碳源的利用效率,其中以酚酸类物质为底物的功能微生物种群数量显著增加。高通量测序结果显示,老参地土壤细菌物种数、丰度与多样性均呈下降趋势,细菌优势门类减少,单个门类优势度上升。生物质炭处理下土壤中细菌丰度与多样性增加,调控了变形菌门、厚壁菌门、疣微菌门、芽单胞菌门的优势度,使其数量变化趋势趋向于新林土。上述分析表明,重茬人参生物量和品质的提高与生物质炭提升土壤中人参生长的关键肥力指标,促进微生物代谢,调控细菌群落结构变化趋势有关。综上,生物质炭对老参地土壤表现出良好的修复、改良作用,适量增施生物质炭有利于老参地土壤质量的调节与恢复。     

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods

Viruses are highly abundant in temperate soils, ranging from 10⁷ to 10⁹?g^?1, and outnumbering soil bacteria from 5- to over 1,000-fold. In order to determine the potential impacts of viruses on soil microbial communities, it is important to establish reliable methods for comparing changes in viral abundances within and across soil samples. The goals of this study were to optimize extraction-enumeration methods to accurately determine viral abundances in a range of soil types, to evaluate the feasibility of simultaneously enumerating bacterial cells and virus particles using a single extraction procedure, and to assess the utility of flow cytometry (FCM) for enumerating virus particles in soil extracts. Comparisons of extraction approaches indicated that sonication or blender extraction of soils with potassium citrate buffer yielded the highest viral abundances for most soil types. Combined viral and bacterial extractions underestimate abundances compared to separately-optimized extractions for each. Flow cytometric counts were anywhere between 350- and 1,400-fold higher than epifluorescence microscopy (EFM)-based counts for the same soil. Trends in viral abundance across soil types were different from those via EFM, and different relationships between viral abundance and soil properties were observed depending on the enumeration method. Thus, FCM is not currently recommended for enumeration of viruses in soil extracts. Based on EFM results, soil moisture and organic matter content were the most important factors determining viral abundance in soils.     

Unique community structure of viruses in a glacier soil of the Tianshan Mountains,China

Purpose

Glaciers of the Tianshan Mountains have been geographically isolated for a long time with little human interference. This study aimed to understand the viral community structures and their ecological functions in a unique glacier soil.

Materials and methods

The abundances of purified virus particles and bacteria in the glacier soil were examined using epifluorescence microscopy and quantitative PCR of the 16S rRNA gene, respectively. Metagenomic analysis was employed to investigate the taxonomic and functional compositions as well as the phylogenetic relationship of the functional genes of the viruses in the glacier soil.

Results and discussion

A total of eight double-stranded DNA (dsDNA) virus families were identified in the glacier soil, with Siphoviridae, Podoviridae, and Myoviridae being the more abundant families. The diverse dsDNA viruses and few ssDNA and other types of viruses formed the unique community structure of viruses in the Tianshan Mountains glacier soil. The functional genes identified from the virome mainly belonged to phage-related proteins. The phage terminase of Caudovirales presented high diversity, and its amino acid sequences were different from those in other environments.

Conclusions

The results showed a unique viral diversity and taxonomic composition in the glacier soil, which suggests the significant ecological role of Caudovirales in this environment.

     

分析技术在土壤微塑料研究中的应用现状

微塑料污染已成为环境领域研究的热点问题。受采样、前处理和分析技术的限制,现有研究中检测到的微塑料尺寸普遍较大。定量分析技术不够成熟,文献数据之间的可比性较差。复杂组分和表面附着物导致土壤微塑料的分析检测存在更大的挑战。为更好地掌握研究现状与发展趋势,本文从光谱分析、热分析、显微分析等角度分类,对土壤微塑料研究中的分析技术进行了解析、对比和总结。光谱分析对微塑料进行定性和数量统计,常见的有傅里叶变换红外光谱法和拉曼光谱法。热分析用于组分鉴定和质量分析,具体分为裂解气质联用和热重波谱联用。显微分析则对形貌和尺寸进行表征,包括光学显微镜和电子显微镜两种。提出微塑料分析技术越来越丰富,但是针对土壤微塑料的分析是一项复杂的工作。分析技术的标准化是评价和治理微塑料污染的关键;现有的土壤微塑料检测方法各有利弊。组合或联用技术的使用有望更高效、精准地实现对土壤微塑料定性定量分析;应从需要解决的科学问题出发,根据研究目的合理选择分析技术;部分分析技术在土壤微塑料的实际测定有待于进一步的探索与验证。     

Strengthening Analytical Support in Agricultural Research

The need for analytical support in agricultural research and development has long been recognized, especially for soil fertility evaluation and management, assessment of crop and food quality, and selection and breeding of nutritious food staples. In addition, the demand for analytical research support in the general areas of agriculture interfacing with human health and environmental quality has greatly increased in recent years. The trend for increased demand for analytical support will most likely continue in the future. To meet such diverse, increasing demands for analytical support, we need to upgrade infrastructure facilities and simultaneously teach and train students and young researchers in the use of modern analytical tools. This is prerequisite to providing timely, efficient, and effective analytical support, as such support is the key to monitoring, assessing, and maintaining soil, food, and environmental quality and to breeding nutritious food staples.     

Improved cadmium sorption isotherms by the determination of initial contents using the radioisotope 109Cd

Cadmium (Cd) sorption isotherms were estimated by two different analytical approaches to assess the influence of initial Cd concentrations of soil matrix on the sorption of added Cd. For the laboratory experiments a heterogeneous set of samples was collected to include a wide range of different initial Cd concentrations. Comparison of both analytical methods (conventional analysis, radioanalysis) resulted in a strong conformity of Cd contents in solution at equilibrium. The calculated Cd concentrations in the soil solid phase differ according to the analytical approach for considering the initial contents. The determination of the initial contents by the proposed radioanalytical method with ¹⁰⁹Cd resulted in long linear Freundlich‐isotherms, even in the low concentration range. Thus, radioanalysis seems to be the most suitable method to recognise the initial contents of Cd in soil. EDTA extractable Cd represent the initial concentrations, which are averaged over solid and liquid phase. However, depending on the sorption characteristics of the soil these rates vary. In the investigated set of soil samples 52.3 to 99.3% of Cd must be added to the solid phase.     

Determining soil organic carbon for agricultural soils: a comparison between the Walkley & Black and the dry combustion methods (north Belgium)

Mapping soil organic carbon (SOC) and establishing any change over time are important because of CO₂ fluxes between soil and atmosphere and cropland decreases in SOC. The latter is one of the main causes of soil fertility decline and increased erodibility. As most analytical methods underestimate total SOC content, correction factors are needed to avoid methodological bias when comparing SOC data from sampling campaigns using different analytical procedures. The traditional method for SOC analysis used to be, and in most cases still is wet oxidation in potassium dichromate, better known as the Walkley & Black method. In this study, we aim to estimate correction factors for the classic and modified version of the Walkley & Black method for different land use and soil type combinations for agricultural soils in north Belgium. General correction factors of 1.47 for the classic Walkley & Black method and 1.20 for the modified Walkley & Black method are proposed. The results show that sandy grassland soils are characterised by lower recoveries than silt loam grassland soils. Furthermore, the correction factor appears to increase with soil wetness.     

Contribution of soil components to adsorption of Pepper Mild Mottle Virus by Japanese soils

The Pepper Mild Mottle Virus (PMMoV) is a soil-borne virus that causes the mosaic disease to Capsicum ssp. This virus disease had been controlled by soil fumigation using methyl bromide, but the method was banned in 2005. Therefore, a new management and control technology that replaces methyl bromide is required. In the present study, the adsorption of PMMoV by soils that is considered to be one of the most important factors of the virus inactivation was examined. We used eight soil samples with different types of clay compositions and humus contents for the PMMoV adsorption experiments at three different pH levels (pH 4, 5 and 7). Large amounts of PMMoV particles were adsorbed by the soil samples with a low humus content at the low pH. This was attributed to the increase in the positive charges of the soil samples. On the other hand, low virus adsorptions were observed at the pH levels in the soils with a high organic matter content. There were close negative correlations (P < 0.05) between the PMMoV adsorption by the soils and the humus content of the soil samples. We considered that the inhibitory effect of humus against the virus adsorption is rather important in most soils in Japan.     

Assessment of Spatial Distribution of Selected Soil Properties using Geospatial Statistical Tools

To gain additional knowledge and better understand forest soil management on a small scale, geostatistical analytical tools were employed to examine the spatial distribution in dry aggregate mean weight diameter (MWD) and other selected soil properties and to assess the possible relationships between MWD and other soil properties. Selected properties of forest soils collected along a 300-m transact in the Nimbia Forest Reserve of Nigeria exhibited moderate to high variability in distribution with sodium ion displaying the greatest variability [coefficient of variation (CV, 91.2%)] and principal component analysis revealed the exchange complex cluster as influencing total variation of field soil properties. The autocorrelation function showed significant spatial correlation from 1 lag in soil organic carbon up to 17 lags (51 m) in soil moisture content (θ). The spherical and Gaussian semivariogram models described the spatial structure of most soil properties; however, for clay, cation exchange capacity (CEC), and soil organic carbon (SOC), an exponential model analyzed their spatial dependence.     

温室主要结构参数对其气候的影响

本文描述了温室气候的动态模型及其精确分析解,基于转换因子变化的分析解,研究了温室主要十个参数对其气侯的影响。结果表明,影响最大的参数为温室覆盖材料对太阳辐射和热辐射的透射率以及作物占温室土壤表面积的比例。此研究将对室内模拟条件对相应检测结果的调整起重要作用。     

精准农业土壤养分与水稻产量关系模型研究

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