Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.
Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.
复制标题
DOI：
10.3389/fmicb.2015.00358
复制
发表时间：
2015
影响因子：
5.2
通讯作者：
Vogel TM
中科院分区：
文献类型：
--
作者：
Delmont TO;Eren AM;Maccario L;Prestat E;Esen ÖC;Pelletier E;Le Paslier D;Simonet P;Vogel TM
尽管广泛的直接测序工作和先进的分析工具，利用宏基因组学从土壤中重建微生物基因组一直具有挑战性，因为在这个系统中发现的基因组具有巨大的多样性和相对均匀的分布。在这里，我们使用富集技术，通过在23个不同的微生物环境中进行4个月的物理和化学胁迫，试图在测序之前降低土壤微生物组的复杂性。在处理结束时对这些微生物进行宏基因组分析，使用标准从头组装技术获得540 Mb的组装（总共559,555个基因和29,176个功能），从中我们可以恢复新的细菌基因组，质粒和噬菌体。获得的基因组分别为Leifsonia （n = 2）、Rhodanobacter （n = 5）、Acidobacteria （n = 2）、Sporolactobacillus （n = 2）、ktedonobacteria （n = 1）、Streptomyces （n = 3）、Burkholderia （n = 2，包括具有汞抗性的巨型质粒）。组装的基因组平均为5.9 Mb，在原始土壤微生物组中的相对丰度从罕见（<0.0001%）到相对丰富（>0.01%）不等。此外，我们在地理位置较远的地方收集的样品中检测到它们，特别是在温带土壤中，与来自高纬度土壤和沙漠的样品相比，它们更多地来自温带土壤。据我们所知，这项研究是第一次成功地尝试直接从土壤样本中组装多个细菌基因组。我们的研究结果表明，开发相关的富集条件可以刺激环境基因组的发现，这是不可能实现的规范方法，只关注测序后的数据处理。
Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.