Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes
Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes
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DOI：
10.1128/aem.00102-12
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发表时间：
2012-05-01
影响因子：
4.4
通讯作者：
Brady, Sean F.
中科院分区：
文献类型：
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作者：
Reddy, Boojala Vijay B.;Kallifidas, Dimitris;Brady, Sean F.
近年来，估计存在于地球上的细菌物种数量急剧增加。这种新认识的物种多样性提出了细菌天然产物生物合成多样性也被以前基于培养的研究大大低估的可能性。在这里，我们比较454焦测序的非核糖体肽腺苷酸化结构域，I型聚酮酮酮合酶结构域，和II型聚酮酮酮合酶α基因片段扩增从粘粒文库构建的DNA分离自三个不同的干旱土壤。虽然16S rRNA基因序列分析表明这些克隆的宏基因组包含来自主要细菌门的相似分布的DNA，但我们发现它们包含几乎完全不同的次级代谢物生物合成基因序列集合。当以85%的同一性分组时，只有1.5%的腺苷酸化结构域、1.2%的酮合酶和9.3%的酮合酶α序列簇包含来自所有三个宏基因组的序列。虽然生物合成基因序列多样性和这些基因所在的基因簇编码的代谢产物的多样性之间不太可能存在简单的相关性，但我们的分析进一步表明，一个土壤宏基因组中的序列与另一个宏基因组中的序列是如此遥远，以至于在许多情况下，它们可能来自功能不同的基因簇。即使在生态相似的环境中发现的生物合成基因的集合之间观察到的显着差异表明，原核生物天然产物的生物合成多样性是，像细菌物种的多样性，可能远远大于从文化为基础的研究。
The number of bacterial species estimated to exist on Earth has increased dramatically in recent years. This newly recognized species diversity has raised the possibility that bacterial natural product biosynthetic diversity has also been significantly underestimated by previous culture-based studies. Here, we compare 454-pyrosequenced nonribosomal peptide adenylation domain, type I polyketide ketosynthase domain, and type II polyketide ketosynthase alpha gene fragments amplified from cosmid libraries constructed using DNA isolated from three different arid soils. While 16S rRNA gene sequence analysis indicates these cloned metagenomes contain DNA from similar distributions of major bacterial phyla, we found that they contain almost completely distinct collections of secondary metabolite biosynthetic gene sequences. When grouped at 85% identity, only 1.5% of the adenylation domain, 1.2% of the ketosynthase, and 9.3% of the ketosynthase alpha sequence clusters contained sequences from all three metagenomes. Although there is unlikely to be a simple correlation between biosynthetic gene sequence diversity and the diversity of metabolites encoded by the gene clusters in which these genes reside, our analysis further suggests that sequences in one soil metagenome are so distantly related to sequences in another metagenome that they are, in many cases, likely to arise from functionally distinct gene clusters. The marked differences observed among collections of biosynthetic genes found in even ecologically similar environments suggest that prokaryotic natural product biosynthesis diversity is, like bacterial species diversity, potentially much larger than appreciated from culture-based studies.