Fuchsman Clara A, Collins Roy Eric, Rocap Gabrielle, Brazelton William J
School of Oceanography, University of Washington, Seattle, WA, United States of America.
College of Fisheries and Ocean Sciences, University of Alaska-Fairbanks, Fairbanks, AK, United States of America.
PeerJ. 2017 Sep 29;5:e3865. doi: 10.7717/peerj.3865. eCollection 2017.
Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).
We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.
Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.
水平基因转移，即遗传物质在不同物种生物体之间的转移与整合，在微生物适应环境过程中发挥着重要作用，但作用程度尚未得到充分量化。先前的研究表明，基因组大小与水平转移基因的数量密切相关。在此，我们探讨基因组大小如何干扰水平基因转移的量化，因为生物体随时间积累的基因数量取决于其进化历史和生态环境（例如，其适应的营养条件）。
我们通过首先统计448个细菌基因组和57个古菌基因组之间的双向BLAST比对命中数来寻找共享基因，从而研究古菌和细菌之间的水平基因转移。然后，我们使用DarkHorse算法，一种基于概率的、谱系加权方法（Podell和Gaasterland，2007年），在这些共享基因中识别潜在的水平转移基因。通过消除细菌基因组大小的影响，我们鉴定出了一些细菌，它们相对于其基因组大小而言，与古菌共享的基因数量异常之多。有趣的是，生活在厌氧和/或高温条件下的古菌和细菌更有可能共享异常大量的基因。然而，高盐环境并未被发现对共享基因数量有显著影响。共享基因（经基因组大小校正的双向BLAST比对命中数）和转移基因（由DarkHorse算法鉴定）的数量密切相关。因此，生活在厌氧和/或高温条件下的古菌和细菌更有可能共享水平转移基因。这些水平转移基因在参与能量转换以及无机离子和氨基酸的运输与代谢的基因中占比过高。
厌氧和嗜热细菌与古菌共享异常大量的基因。这主要是由于基因从古菌水平转移到细菌。一般来说，这些转移来自生活在与接收基因的细菌相似的氧气和温度条件下的古菌。古菌和细菌之间水平基因转移的潜在热点包括温泉、海洋沉积物和油井。水平转移的冷点包括稀释的、需氧的、中温环境，如海洋和淡水表层水。
