Occidental College, United States.
University of Queensland, Australia.
Comput Struct Biotechnol J. 2014 Dec 13;13:18-23. doi: 10.1016/j.csbj.2014.12.001. eCollection 2015.
RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments ('tanks') formed by tropical bromeliads from Costa Rica. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to the specific presence of eukaryotes. Bacteria from 25 phyla appeared to comprise the majority of transcripts in one tank (Wg24), compared to only 14 phyla in the other (Wg25). Conversely, eukaryotes from only 16 classes comprised the majority of transcripts in Wg24, compared to 24 classes in the Wg25, revealing a greater eukaryote diversity in the latter. Given that these bromeliads had tanks of similar size (i.e. vertical oxygen gradient), and were neighboring with presumed similar light regime and acquisition of leaf litter through-fall, it is possible that pH was the factor governing these differences in bacterial and eukaryotic communities (Wg24 had a tank pH of 3.6 and Wg25 had a tank pH of 6.2). Archaeal diversity was similar in both tanks, represented by 7 orders, with the exception of Methanocellales transcripts uniquely recovered from Wg25. Based on measures of FPKG (fragments mapped per kilobase of gene length), genes involved in methanogenesis, in addition to a spirochaete flagellin gene, were among those most highly expressed in Wg25. Conversely, aldehyde dehydrogenase and monosaccharide-binding protein were among genes most highly expressed in Wg24. The ability to observe specific presence of insect, plant, and fungi-associated RNA-viruses was unexpected. As with other techniques, there are inherent biases in the use of RNA-Seq, however, these data suggest the possibility of understanding the entire community, including ecological interactions, via simultaneous analysis of microbial, eukaryotic, and viral transcripts.
RNA-Seq 被用于研究来自哥斯达黎加的热带凤梨科植物形成的集水区（“水箱”）中的微生物、真核生物和病毒群落。总共观察到了具有广泛细菌、古菌和真核生物分类归属的转录本，以及与真核生物特定存在相关的 RNA 病毒。在一个水箱（Wg24）中，似乎有 25 个门的细菌构成了大多数转录本，而另一个水箱（Wg25）中只有 14 个门。相反，在 Wg24 中，只有 16 个纲的真核生物构成了大多数转录本，而在 Wg25 中则有 24 个纲，这表明后者的真核生物多样性更大。鉴于这些凤梨科植物的水箱大小相似（即垂直氧梯度），并且与假定具有相似光照条件和通过叶凋落物获取的叶片相邻，因此 pH 值可能是控制这两个水箱中细菌和真核生物群落差异的因素（Wg24 的水箱 pH 值为 3.6，而 Wg25 的水箱 pH 值为 6.2）。两个水箱中的古菌多样性相似，由 7 个目代表，除了 Methanocellales 转录本是唯一从 Wg25 中回收的。根据 FPKG（基因长度每千碱基映射的片段）的测量值，除了螺旋体鞭毛蛋白基因外，参与甲烷生成的基因是在 Wg25 中表达最高的基因之一。相反，醛脱氢酶和单糖结合蛋白是在 Wg24 中表达最高的基因之一。能够观察到昆虫、植物和真菌相关 RNA 病毒的特定存在是出乎意料的。与其他技术一样，RNA-Seq 存在固有偏见，但是这些数据表明，通过同时分析微生物、真核生物和病毒转录本，有可能了解整个群落，包括生态相互作用。
