Genomic determinants of soil depth niche partitioning in Gagatemarchaeaceae, a novel family of deeply-rooted Thaumarchaeota
Genomic determinants of soil depth niche partitioning in Gagatemarchaeaceae, a novel family of deeply-rooted Thaumarchaeota
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DOI：
10.1101/2023.03.08.531495
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发表时间：
2023-03
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影响因子：
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通讯作者：
Paul O. Sheridan;Yiyu Meng;T. Williams;C. Gubry-Rangin
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作者：
Paul O. Sheridan;Yiyu Meng;T. Williams;C. Gubry-Rangin
尽管酸性土壤中存在丰富的非氨氧化奇古菌谱系，但对陆地环境中根深蒂固的非氨氧化奇古菌谱系的了解却很少。在这里，15个新的根深蒂固的奇古菌基因组由酸性表土（0-15厘米）和底土（30-60厘米）组装而成，其中大多数对应于陆地上流行的Gagatemarchaeaceae科的两个属（以前称为奇古菌组I.1c）。与之前的预测不同，代谢注释表明 Gagatemarchaeaceae 进行有氧呼吸并使用各种有机碳源。表土和下土谱系之间的进化物种形成发生在 Gagatemarchaeaceae 历史的早期，具有显着的代谢和基因组性状差异。进化机制的重建表明，表土 Gagatemarchaeaceae 中的基因组扩展是由于广泛的早期横向基因获得，随后在整个进化史上逐渐进行的基因复制所致。利用扩展的基因组多样性重建祖先性状也驳斥了之前关于奇古菌嗜热祖先的假设。最终，这项研究为研究驱动空间相关生态系统之间的生态位划分的机制提供了一个有吸引力的模型。
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15cm) and subsoils (30-60 cm), most of them corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c). Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary speciation between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also refuted the previous hypothesis of a Thaumarchaeota thermophilic ancestor. Ultimately, this study provides an attractive model for studying mechanisms driving niche partitioning between spatially related ecosystems.