Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami.
Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami.
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DOI：
10.1186/s12864-016-2380-4
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发表时间：
2016-01-14
期刊：
影响因子：
4.4
通讯作者：
Iwasaki W
中科院分区：
文献类型：
--
作者：
Hiraoka S;Machiyama A;Ijichi M;Inoue K;Oshima K;Hattori M;Yoshizawa S;Kogure K;Iwasaki W
2011年的东日本大地震引发了巨大的海啸，淹没了东日本太平洋沿岸沿着的大片土地，土壤环境发生了巨大变化。然而，受海啸影响的土壤在基因组水平上的微生物特征在很大程度上仍然未知。在这项研究中，我们从土壤样品中分离微生物，使用一般的低营养和海水为基础的媒体，调查在海啸影响的土壤中的微生物特征。正如预期的那样，从受海啸影响的土壤中分离出的菌株比未受影响的土壤中分离出的菌株在基于海水的培养基中生长的比例更大。在普通低营养和海水培养基中均可培养的菌株均属于节杆菌属。最重要的是，四个分离的节杆菌菌株的全基因组测序揭示了铁载体合成基因从其基因组的独立损失。铁载体是低分子量的铁螯合化合物，分泌用于铁吸收;因此，铁载体合成基因的丢失表明这些菌株已经适应了高铁浓度的环境。事实上，化学分析证实了调查的土壤样品富含铁，培养实验证实了其中一些菌株在铁限制培养基中的可培养性较弱。此外，宏基因组分析表明，在受海啸影响的土壤样本中，过度表达了与酸化相关的基因，以及存在致病性和海洋生物属以及与耐盐性相关的基因。总的来说，目前的研究结果将提供一个例子的微生物特征的土壤被海啸，这可能会给微生物适应剧烈的环境变化的洞察。对海啸后的微生物生态学进行进一步分析，以更深入地了解陆地微生物生态系统的恢复过程。本文的在线版本（doi：10.1186/s12864-016-2380-4）包含补充材料，可供授权用户使用。
The Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil. As expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experiments confirmed weak cultivability of some of these strains in iron-limited media. Furthermore, metagenomic analyses demonstrated over-representation of denitrification-related genes in the tsunami-affected soil sample, as well as the presence of pathogenic and marine-living genera and genes related to salt-tolerance. Collectively, the present results would provide an example of microbial characteristics of soil disturbed by the tsunami, which may give an insight into microbial adaptation to drastic environmental changes. Further analyses on microbial ecology after a tsunami are envisioned to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems. The online version of this article (doi:10.1186/s12864-016-2380-4) contains supplementary material, which is available to authorized users.