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土壤微生物宏基因组研究现状——基于Citespace文献计量分析
Research Status of Soil Microbial Metagenomics: Based on Citespace Bibliometric Analysis
以2005—2020年中国知网(CNKI)和Web of Science数据库为文献来源,采用文献计量方法对土壤微生物宏基因组学研究现状进行统计分析。结果表明,中外学者采用高通量技术进行土壤微生物宏基因组研究的报道持续增加,研究对象以细菌为主,其次是真菌;研究的生境涉及根际、沉积物等。英文文献的研究机构和作者之间合作紧密,而中文文献的研究机构与作者之间的合作以中科院体系为主。在文献质量方面,以美国学者所发表文献的引用率最高,而中国学者所发文献中引用率排名靠前的文献较少。未来基于高通量测序的土壤微生物宏基因组研究应进一步加强机构与人员合作,注重学科交叉,以创新的思维在基因、功能等不同水平上全面分析了解土壤微生物,以深入挖掘其生态学功能,为生态系统的可持续发展提供服务。
This research used China National Knowledge Network (CNKI) and Web of Science database from 2005 to 2020 as the document source, and bibliometric method was used to analyze the current status of soil microbial metagenomics research field. The results show that the studies on soil microbial metagenomics conducted by Chinese and foreign scholars using high-throughput technology increase continuously. The research objects are mainly about bacteria and fungi. The research habitats involve rhizosphere, sediment, and etc. There is close cooperation between research institutions and authors of English publications, while the cooperation between institutions and authors of Chinese publications is mainly centered on the Chinese Academy of Sciences system. In terms of publication quality, the citation rate of the literature published by American scholars is the highest, while the citation rate of literature published by Chinese scholars is relatively low. Based on the results of literature analysis, we suggest that the future high-throughput sequencing-based soil microbial metagenomics research should focus on interdisciplinary study, further strengthen cooperation among institutions and researchers, and use innovative thinking to comprehensively analyze soil microbial at different levels such as gene and function level, thus deeply exploring the ecological functions of soil microorganisms and providing services for the sustainable development of the ecosystem.
土壤微生物 / 宏基因组 / 文献计量分析 / 中国知网 / Web of Science {{custom_keyword}} /
soil microorganism / metagenomic / bibliometric analysis / CNKI / Web of Science {{custom_keyword}} /
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Soil bacterium DNA was isolated by minor modifications of previously described methods. After purification on hydroxyapatite and precipitation with cetylpyridinium bromide, the DNA was sheared in a French press to give fragments with an average molecular mass of 420,000 daltons. After repeated hydroxyapatite purification and precipitation with cetylpyridinium bromide, high-pressure liquid chromatography analysis showed the presence of 2.1% RNA or less, whereas 5-methylcytosine made up 2.9% of the total deoxycytidine content. No other unusual bases could be detected. The hyperchromicity was 31 to 36%, and the melting curve in 1 X SSC (0.15 M NaCl plus 0.015 M sodium citrate) corresponded to 58.3 mol% G+C. High-pressure liquid chromatography analysis of two DNA samples gave 58.6 and 60.8 mol% G+C. The heterogeneity of the DNA was determined by reassociation of single-stranded DNA, measured spectrophotometrically. Owing to the high complexity of the DNA, the reassociation had to be carried out in 6 X SSC with 30% dimethyl sulfoxide added. Cuvettes with a 1-mm light path were used, and the A275 was read. DNA concentrations as high as 950 micrograms ml-1 could be used, and the reassociation rate of Escherichia coli DNA was increased about 4.3-fold compared with standard conditions. C0t1/2 values were determined relative to that for E. coli DNA, whereas calf thymus DNA was reassociated for comparison. Our results show that the major part of DNA isolated from the bacterial fraction of soil is very heterogeneous, with a C0t1/2 about 4,600, corresponding to about 4,000 completely different genomes of standard soil bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)
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