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1.
江西典型红壤区土壤细菌基因组文库构建及功能初步分析 总被引：3，自引：0，他引：3
地球上的微生物,仅原核生物细胞总数就大约在4×1030～6×1030,包含的独立基因型在106～108种之间[1].因此,微生物所具备的分类、功能、遗传和系统发育等多样性在维持生物圈生态平衡和为人类提供资源方面起着重要的作用[2].然而长期以来由于受到研究方法和手段的限制,土壤中绝大多数微生物的功能还不清楚.环境样品的宏基因组学(metagenomics)是对环境样品中微生物群体基因组进行的分析,该方法在众多用于获得未培养微生物的生理和遗传特性的方法中,逐渐显示出强大的优势[3,4].国外已有从不同环境样品的宏基因文库中,通过功能性筛选获得新的抗生素、脂肪酶、丁质酶、膜蛋白、4-羟基丁酸脱氢酶等合成基因或相关基因,以及对群落结构组成和功能进行分析的报道[5～9].国内也逐步开始有相关研究[10,11]. 相似文献
2.
土壤宏基因组学研究方法与进展 总被引：3，自引：0，他引：3
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。 相似文献
3.
土壤微生物分离新技术的研究进展 总被引：1，自引：0，他引：1
土壤是环境微生物学研究中最具挑战性的环境,也是生物分子、遗传资源开发的热点区域。在"宏-组学"方法快速发展的今天,土壤微生物分离培养技术在微生物环境功能研究、代谢途径的阐明、特定功能的验证及基础实验和生产实践的应用等方面仍然发挥着重要作用。本文首先分析了大多数环境微生物不能被分离培养的几个原因。然后重点综述了近年来在土壤微生物分离培养技术方面的探索,主要包括生长培养基的优化和重新设计如培养基稀释分离、添加生长限制因子、更换凝固剂等,在延长培养时间、改善含氧量、降低培养温度等方面对生长条件进行改进,采用"扩散盒"、"原位培养陷阱"等技术对微生物进行天然环境原位培养,对环境微生物群体培养和共培养,利用"宏基因组学""宏蛋白质组学"等非培养技术辅助分离等。最后,作者对未来土壤微生物分离研究的方向提出了自己的建议。 相似文献
4.
有机磷农药污染土壤的微生物降解研究进展 总被引：3，自引：1，他引：3
有机磷农药是目前我国使用量最大的农药之一,严重污染环境和生态系统,并通过食物链在生物体内富集,进而危害人类健康。微生物降解技术具有降解效率高、代谢途径多、无二次污染的优势,是目前清除环境中有机磷农药的主要手段,能有效降低有机磷农药的危害。目前有机磷农药的降解微生物主要是通过实验室纯培养方法获得,与自然生态环境中存在的降解功能性微生物信息差异较大,而利用不可培养方法识别功能性微生物的技术具有广阔的应用前景。本文从有机磷农药的使用情况及引发的环境问题出发,概述了有机磷农药在土壤中的迁移转化途径,稳定同位素探测技术和磁性纳米材料等不可培养方法对有机磷农药降解功能性微生物的识别,微生物降解有机磷农药污染土壤的功能基因、降解途径及降解机理;探讨了植物–微生物联合修复在有机磷农药污染土壤修复中的作用,并分析了环境因子及农药自身性质对有机磷农药降解的影响;最后,讨论了微生物降解技术存在的问题及今后研究方向。 相似文献
5.
棉花根际促生细菌的研究进展 总被引：1，自引：0，他引：1
综述了根际促生细菌(PGPR)的概念、研究手段、基因标记技术和荧光原位杂交技术在研究棉花根际促生细菌中的应用.植物根系可以分泌各种对微生物有益的物质,吸引微生物在根际的聚集.棉花凝集素对根际促生细菌菌株的胞外多糖具有凝集作用,在棉花根际促生细菌与棉花根部相互识别过程中具有重要作用,可以利用棉花凝集素作为筛选工具筛选对棉花具有促生作用的根际促生细菌菌株.基因标记技术证明棉花根际促生细菌能高密度地定殖在棉花根部,对棉花的生长起促进作用,并能抑制某些植物病原菌及根际有害微生物.分子生物学技术在微生物生态学领域的应用促进了棉花根际促生细菌的研究和应用,可以利用棉花根际促生细菌研发微生物肥料. 相似文献
6.
纤维堆囊菌（S.cellulosum）属于粘细菌中的堆囊菌属,它们能产生丰富的次级代谢产物,而且是目前基因组最大的原核生物,现已测序的S.cellulosum So ce56和So 0157-2分别拥有13.03 Mb和14.78 Mb的环状染色体。本文阐述了这两株纤维堆囊菌在序列的组装验证和基因组的分析注释等方面的完成情况,以及人们在测序的基础上,对其展开的结构基因组学、比较基因组学和功能基因组学的研究。通过介绍这两株已测序纤维堆囊菌的基因组学研究现状,我们总结了从纤维堆囊菌的全基因组序列中挖掘遗传信息的方法,为发现纤维堆囊菌中新的功能基因提供一些参考。 相似文献
7.
从土壤中提取土壤总DNA,切割成一定长度的DNA片段并连接到载体上,然后转化宿主菌,形成一个重组DNA文库即宏基因组（metagenome）文库.目前对宏基因组的研究在国际上是土壤微生物学研究的前沿领域和热点.文库构建后可以根据宿主细菌获得的功能筛选相应的克隆;也可以用已知的探针分离目的基因片段,加上表达调控元件后获取活性产物,所以通过宏基因组文库可以规避微生物培养的限制而寻找新的功能基因或者直接筛选活性物质;在早期宏基因组还被用来研究土壤微生物的遗传多样性.因此构建宏基因组文库是研究微生物分子生态学和开发微生物资源的强有力工具.本研究从土壤中直接分离DNA,部分酶切后分别回收2～6kb和6～9kb片段,然后分别与pUC19质粒载体连接,连接产物转化大肠杆菌DH5α构建了土壤宏基因组文库,实验中比较了不同DNA片段长度和不同的转化方法对文库构建的影响. 相似文献
8.
参与土壤氮素循环的微生物功能基因多样性研究进展 总被引：12，自引：2，他引：12
土壤氮素循环是生物地球化学循环的重要组成部分, 不但影响着土壤生产力和可持续发展, 还影响着全球环境变化.土壤微生物在土壤氮循环中发挥着不可替代的作用, 参与了包括固氮作用、氨化作用、硝化作用和反硝化作用等重要生态过程.近十年中, 分子生物学技术的发展为从功能基因角度研究与土壤氮循环密切相关的微生物功能群结构、组成和丰度的变化提供了新的契机.本文综述了参与土壤氮循环的微生物功能基因多样性研究进展, 并展望了未来发展方向. 相似文献
9.
植物根际微生物组的研究进展 总被引：2，自引：1，他引：1
根际微生物组(rhizosphere microbiome),是植物从其种子库土壤微生物组中有选择性地招募在根际聚集的动态微生物集群.随着近年来高通量测序技术、宏基因组学等的飞速发展,根际微生物组与植物宿主及土壤微生物组间的紧密联系引起了全球关注和研究热潮.根际微生物组被视作植物第二基因组,其与植物间的互作极为复杂,有... 相似文献
10.
以柴油为唯一碳源,在富集、驯化培养基础上,从胜利油田石油污染土壤中筛选出一株柴油降解微生物WS14,通过外观形貌、Biolog鉴定等生理生化分析以及16S rRNA基因序列分析,确定该微生物为不动杆菌属（Acinetobacter sp.）。通过对筛选到柴油降解菌的生长因子研究发现：适合WS14菌株生长的最佳pH值为6.0～8.5,适宜温度为35℃,最佳培养时间为72h,并且柴油含量为11.5%时菌株的生长量最大;实验结果显示,WS14菌株对高盐和高含量柴油具有一定的耐受性,能够在5%含盐量和30%柴油含量的环境生长。 相似文献
11.
Gleason FH Crawford JW Neuhauser S Henderson LE Lilje O 《Soil biology & biochemistry》2012,45(2):79-88
Zoosporic true fungi have frequently been identified in samples from soil and freshwater ecosystems using baiting and molecular techniques. In fact some species can be components of the dominant groups of microorganisms in particular soil habitats. Yet these microorganisms have not yet been directly observed growing in soil ecosystems. Significant physical characteristics and features of the three-dimensional structures of soils which impact microorganisms at the microscale level are discussed. A thorough knowledge of soil structures is important for studying the distribution of assemblages of these fungi and understanding their ecological roles along spatial and temporal gradients. A number of specific adaptations and resource seeking strategies possibly give these fungi advantages over other groups of microorganisms in soil ecosystems. These include chemotactic zoospores, mechanisms for adhesion to substrates, rhizoids which can penetrate substrates in small spaces, structures which are resistant to environmental extremes, rapid growth rates and simple nutritional requirements. These adaptations are discussed in the context of the characteristics of soils ecosystems. Recent advances in instrumentation have led to the development of new and more precise methods for studying microorganisms in three-dimensional space. New molecular techniques have made identification of microbes possible in environmental samples. 相似文献
12.
O. S. Kukharenko T. G. Dobrovol’skaya A. V. Golovchenko A. L. Stepanov G. V. Matyshak 《Eurasian Soil Science》2009,42(4):426-431
The tundra cryogenic soils of Yamal Peninsula have a high pool of prokaryote microorganisms characteristic of ecosystems where the environmental conditions are unfavorable for microbiological processes. The lowering of the cultivation temperature from 20 to 5°C did not affect the number of bacteria and their taxonomic structure. Psychrotolerant gram-negative bacteria represented by oligotrophs and copiotrophs predominated in the bacterial communities. Among the bacteria of the hydrolytic block, only bacilli were isolated upon cultivation on the media. The species spectrum of the Bacillus genus was determined by the capability of its representatives for growth at low temperatures. The bacteria isolated from the cryogenic soils had a high nitrogenase activity, which increased under the lower cultivation temperature. This fact shows that the majority of the bacteria in tundra soils has adapted to functioning at low temperatures. 相似文献
13.
微生物在众多的自然和人工生态系统中发挥着核心的作用,但能够被培养分离的微生物在大部分生态系统中只占极少一部分,极大地限制了人们对微生物组成、功能及其潜在应用的认识。分子生物学方法,尤其是高通量测序技术应用到微生物生态学研究中,为认识微生物多样性、群落结构组成及其生态功能提供了有利手段。高通量测序作为一种新兴的免培养分子生物学技术,具备检测快速、准确、信息全面丰富等特点。随着高通量测序技术的不断升级换代,测序通量、读长和准确度的不断提升以及成本的大幅下降,该技术在过去十几年间被迅速应用于土壤、水体和肠道等微生物区系的研究中。本文简述了基于高通量测序技术的PCR产物测序技术和宏基因组学测序技术的原理、发展历程、数据分析方法与应用,以及宏基因组学测序技术在病毒学领域的应用,以期为微生物分子生态学研究提供参考。 相似文献
14.
The number of Enterobacteriaceae, with particular attention given to the presence of Escherichia coli and Klebsiella pneumoniae, was determined in hospital effluents and municipal wastewater after various stages of purification. The emission of these microorganisms to the ambient air near wastewater treatment plant (WWTP) facilities and to the river water, which is a receiver of the WWTP effluent, was also studied using fluorescence in situ hybridization (FISH) and cultivation methods. The number of Enterobacteriaceae determined by cultivation and fluorescence methods in different kinds of sewage sample ranged from 0.5?×?10(3) to 2.9?×?10(6)?CFU/ml and from 2.2?×?10(5) to 1.3?×?10(8) cells/ml, respectively. Their removal rates during treatment processes were close to 99?%, but the number of these bacteria in the WWTP outflow was quite high and ranged from 5.9?×?10(3) to 3.5?×?10(4)?CFU/ml and from 1.1?×?10(5) to 6.1?×?10(5) cells/ml, respectively. In the river water and the air samples, the number of Enterobacteriaceae was also high and ranged from 4.1?×?10(3) to 7.9?×?10(3)?CFU/ml and from 3 to 458?CFU/m(3), respectively. The numbers of these microorganisms obtained from fluorescence and cultivation methods were statistically and significantly correlated; however, the analysis of the studied samples indicated that the FISH method gave values up to 10(3)-fold times greater than those obtained by the cultivation method. From a sanitary point of view, this means that the number of viable fecal bacteria is systematically underestimated by traditional culture-based methods. Thus, the FISH proves to be a method that could be used to estimate bacterial load, particularly in air samples and less contaminated river water. 相似文献
15.
Kim SE Moon JS Choi WS Lee EN Lee SH Kim SU 《Journal of agricultural and food chemistry》2010,58(24):12657-12663
The environmental release of genetically engineered microorganisms (GEMs) to improve agriculture or remediate environmental hazards has raised concern over the fate of the organisms and their engineered genes. To detect the microorganisms released into the environment at the molecular level, Bacillus subtilis KB producing iturin and Pseudomonas fluorescens MX1 carrying the moc (mannityl opine catabolism) region from the Agrobacterium tumefaciens were employed as model microorganisms. Using specific fusion primers and the TaqMan probes, qualitative and quantitative detections of the model organisms by PCR and real-time PCR were conducted employing a small-scale soil-core device and pots during the six month period. The data indicate that the model bacteria can be easily detected by qualitative and quantitative methods in the test systems employed, and they do not give significant impacts on the other bacteria in soils on the Southern blotting analysis, although long-term observation may be needed. 相似文献
16.
Tomio Yoshida Rosabel A. Roncal Ellen M. Bautista 《Soil Science and Plant Nutrition》2013,59(2):117-123
Photosynthetic nitrogen-fixing microorganisms help maintain the nitrogen level of soil in rice paddies when environmental factors favor the growth of microorganisms. Our studies showed that blue-green algae in particular have a significant role in nitrogen-fixation in light. The most active nitrogen-fixation by microorganisms occurred in the soil shortly after it had been submerged under light. The longer the submergence, the less nitrogen microorganisms were fixed. In a greenhouse experiment, the fixed nitrogen appeared not to be immediately available to the rice plant. The amount of nitrogen that can be fixed in the field by nitrogen-fixing microorganisms in paddy water was estimated using the acetylene reduction method during the rice-growing period. The amount of nitrogen fixation by these microorganisms is not sufficient to account for the amount of nitrogen uptake by rice during the rice-growing period. 相似文献
17.
Sren Thiele‐Bruhn 《植物养料与土壤学杂志》2003,166(2):145-167
Antibiotics are highly effective, bioactive substances. As a result of their consumption, excretion, and persistence, they are disseminated mostly via excrements and enter the soils and other environmental compartments. Resulting residual concentrations in soils range from a few μg upto g kg–1 and correspond to those found for pesticides. Numerous antibiotic molecules comprise of a non‐polar core combined with polar functional moieties. Many antibiotics are amphiphilic or amphoteric and ionize. However, physicochemical properties vary widely among compounds from the various structural classes. Existing analytical methods for environmental samples often combine an extraction with acidic buffered solvents and the use of LC‐MS for determination. In soils, adsorption of antibiotics to the organic and mineral exchange sites is mostly due to charge transfer and ion interactions and not to hydrophobic partitioning. Sorption is strongly influenced by the pH of the medium and governs the mobility and transport of the antibiotics. In particular for the strongly adsorbed antibiotics, fast leaching through soils by macropore or preferential transport facilitated by dissolved soil colloids seems to be the major transport process. Antibiotics of numerous classes are photodegraded. However, on soil surfaces this process if of minor influence. Compared to this, biotransformation yields a more effective degradation and inactivation of antibiotics. However, some metabolites still comprise of an antibiotic potency. Degradation of antibiotics is hampered by fixation to the soil matrix; persisting antibiotics were already determined in soils. Effects on soil organisms are very diverse, although all antibiotics are highly bioactive. The absence of effects might in parts be due to a lack of suitable test methods. However, dose and persistence time related effects especially on soil microorganisms are often observed that might cause shifts of the microbial community. Significant effects on soil fauna were only determined for anthelmintics. Due to the antibiotic effect, resistance in soil microorganisms can be provoked by antibiotics. Additionally, the administration of antibiotics mostly causes the formation of resistant microorganisms within the treated body. Hence, resistant microorganisms reach directly the soils with contaminated excrements. When pathogens are resistant or acquire resistance from commensal microorganisms via gene transfer, humans and animals are endangered to suffer from infections that cannot be treated with pharmacotherapy. The uptake into plants even of mobile antibiotics is small. However, effects on plant growth were determined for some species and antibiotics. 相似文献
18.
土壤微生物代谢功能多样性是维持土壤生态系统健康的关键。为评价设施蔬菜种植对土壤微生物代谢功能多样性的影响,采用Biolog-Eco微平板法,研究了2个典型设施蔬菜种植市、不同种植年限设施菜地中土壤微生物代谢功能多样性,分析了与碳源利用相关的细菌群落及影响因子。结果表明：两地设施菜地土壤中平均颜色变化率（Average well color development,AWCD）、Shannon指数、Simpson指数和McIntosh指数随着种植年限的增加而降低,但安丘种植14 a和寿光种植10 a菜地土壤不符合此规律。主成分分析发现,两地之间土壤微生物对碳源利用的差异大于不同种植年限之间的差异。相关分析发现,在安丘土壤中,11种碳源（分属糖类、氨基酸类、羧酸类和聚合物类）与不同门细菌显著相关（P<0.05）;Firmicutes是与碳源相关种类最多的细菌,与9种碳源显著相关（P<0.05）。在寿光土壤中,16种碳源（分属糖类、氨基酸类、羧酸类、聚合物类、酚类和胺类）与不同门细菌显著相关（P<0.05）;Latescibacteria是与碳源相关种类最多的细菌,与4种碳源显著相关（P<0.05）。冗余分析发现,Cd是影响安丘土壤微生物碳源利用的最强环境因子,其负作用显著（P<0.01）,有机质（OM）的正作用为显著（P<0.01）。Zn、OM、Cd对寿光土壤微生物碳源利用的负作用显著（P<0.05）,As、pH值的正作用显著（P<0.05）。设施蔬菜长期种植导致土壤微生物代谢功能多样性持续降低,土壤生物质量退化,亟需采取有效耕作措施改善土壤微生态环境,保障设施菜地土壤健康。 相似文献
19.
Makoto Shinohara Chihiro Aoyama Kazuki Fujiwara Atsunori Watanabe Hiromi Ohmori Yoichi Uehara 《Soil Science and Plant Nutrition》2013,59(2):190-203
Hydroponics is an excellent technique for the cultivation of vegetable crops and other plants, but organic fertilizers cannot be used in conventional hydroponic systems, which generally use only inorganic fertilizers, because organic compounds in the hydroponic solutions generally have phytotoxic effects that lead to poor plant growth. Few microorganisms are present in hydroponic solutions to mineralize the organic compounds into inorganic nutrients. In this article a novel and practical hydroponic culture method that uses microorganisms to degrade organic fertilizer in the hydroponic solution has been developed. Soil microorganisms were cultured by regulating the amounts of organic fertilizer and inoculum, with moderate aeration. The microorganisms mineralized organic nitrogen via ammonification and nitrification into nitrate at an efficiency of 97.6%. The culture solution containing the microorganisms was usable as a hydroponic solution, and organic fertilizer could be directly added to it during vegetable cultivation. Vegetables grew well in the organic hydroponic system. Organic hydroponics based on this method is therefore a practical tool for the utilization of organic sources of fertilizer. 相似文献
20.
Nitrogen biomarkers and their fate in soil 总被引：3，自引：0，他引：3
Wulf Amelung 《植物养料与土壤学杂志》2003,166(6):677-686
More than 90 % of the nitrogen (N) in soils can be organically bound, but the mechanisms and rates by which it is cycled have eluded researchers. The objective of this research was to contribute to a better understanding of the origin and transformation of soil organic N (SON) by using amino sugars and the enantiomers of amino acids as markers for microbial residues and/or aging processes. Studied samples presented here comprised (1) soil transects across different climates, (2) arable soils with different duration of cropping, and (3) radiocarbon‐dated soil profiles. The results suggested that increased microbial alteration of SON temporarily results in a sequestration of N in microbial residues, which are mineralized at later stages of SON decomposition. Microorganisms increasingly sequestered N within intact cell wall residues as frost periods shortened. At a mean annual temperature above 12–15 °C, these residues were mineralized, probably due to limitations in additional substrates. Breaking the grassland for cropping caused rapid SON losses. Microbial residues were decomposed in preference to total N, this effect being enhanced at higher temperatures. Hence, climate and cultivation interactively affected SON dynamics. Nevertheless, not all SON was available to soil microorganisms. In soil profiles, L‐aspartic acid and L‐lysine slowly converted into their D‐form, for lysine even at a similar rate in soils of different microbial activity. Formation of D‐aspartate with time was, therefore, induced by microorganisms while that of D‐lysine was not. The racemization of the two amino acids indicates that SON not available to microorganisms ages biotically and abiotically. In native soils, the latter is conserved for centuries, despite N deficiency frequently occurring in living terrestrial environments. Climate was not found to affect the fate of old protein constituents in surface soil. When native grassland was broken for cropping, however, old SON constituents had become available to microorganisms and were degraded. 相似文献