Accessing the Soil Metagenome for Studies of Microbial Diversity

被引:186
作者
Delmont, Tom O. [1 ]
Robe, Patrick [2 ]
Cecillon, Sebastien [1 ]
Clark, Ian M. [3 ]
Constancias, Florentin [1 ]
Simonet, Pascal [1 ]
Hirsch, Penny R. [3 ]
Vogel, Timothy M. [1 ]
机构
[1] Univ Lyon, Lab Ampere, Ecole Cent Lyon, Environm Microbial Genom Grp, F-69134 Ecully, France
[2] LibraGen, F-31400 Toulouse, France
[3] Rothamsted Res, Harpenden AL5 2JQ, Herts, England
基金
英国生物技术与生命科学研究理事会;
关键词
MOLECULAR-WEIGHT DNA; PROKARYOTIC DIVERSITY; PURIFICATION METHODS; EXTRACTION; RNA; BACTERIA; PCR; QUANTIFICATION; POPULATIONS; DISCOVERY;
D O I
10.1128/AEM.01526-10
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
引用
收藏
页码:1315 / 1324
页数:10
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