Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Environ Microbiol Rep. 2012 Apr;4(2):248-56. doi: 10.1111/j.1758-2229.2012.00328.x. Epub 2012 Feb 10.
The extent to which different sequence-based approaches describe environmental microbial communities in comparative studies is an important consideration when deriving inferences from ecological studies. The ability of a targeted metagenomic approach [small subunit (SSU) rRNA pyrosequencing] and shotgun metagenome approaches were compared to identify distinguishing features in dryland soil microbial communities from two different habitats: biological soil crusts (biocrusts) and creosote bush root zones. A parallel comparison was conducted to determine the ability of each approach to detect community differences potentially arising from a more subtle experimental treatment, long-term elevated atmospheric carbon dioxide. As expected, the biocrust datasets were clearly differentiated from root zone datasets using either of the sequencing approaches. However, the composition described by each approach was significantly different. The magnitude of comparative differences due to habitat or elevated CO2 treatment was larger with pyrosequenced SSU datasets or SSU reads recruited from shotgun metagenomes, than from SEED-classified shotgun metagenome reads. Finally, based on prior knowledge of the biocrust communities, the SSU-based datasets more accurately identified the dominant biocrust cyanobacteria sequences compared to the shotgun metagenome datasets.
在进行生态研究推论时，不同基于序列的方法在比较研究中描述环境微生物群落的程度是一个重要的考虑因素。靶向宏基因组方法（小亚基（SSU）rRNA 焦磷酸测序）和 shotgun 宏基因组方法的能力进行了比较，以确定来自两个不同生境的旱地土壤微生物群落的特征：生物土壤结皮（生物结皮）和石南灌丛根区。进行了平行比较，以确定每种方法识别可能由于更细微的实验处理（长期升高的大气二氧化碳）引起的群落差异的能力。正如预期的那样，使用任何一种测序方法都可以清楚地区分生物结皮数据集和根区数据集。然而，每种方法所描述的组成明显不同。由于栖息地或升高的 CO2 处理而引起的比较差异的幅度，使用焦磷酸测序 SSU 数据集或从 shotgun 宏基因组中招募的 SSU 读段，比从 SEED 分类的 shotgun 宏基因组读段要大。最后，基于对生物结皮群落的先验知识，基于 SSU 的数据集比 shotgun 宏基因组数据集更准确地识别了主要的生物结皮蓝细菌序列。
