Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065.
Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3757-62. doi: 10.1073/pnas.1318021111. Epub 2014 Feb 18.
In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type-specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.
在这项研究中，我们比较了美国西南部和东北部不同环境中 96 个土壤微生物组的生物合成基因丰富度和多样性。从这些微生物组中扩增的非核糖体肽腺苷酸化 (AD) 和聚酮合酶 (KS) 结构域片段的 454 焦磷酸测序为评估不同土壤环境中次生代谢物生物合成多样性的变化提供了一种手段。通过土壤成分和 AD 和 KS 扩增子丰富度分析，我们确定了具有较高生物合成潜力的土壤类型。总的来说，干旱土壤表现出最丰富的观察到的生物合成多样性，而半咸沉积物和松林土壤则表现出最少的生物合成多样性。通过将单个环境扩增子序列映射到功能表征的生物合成基因簇中获得的序列，我们确定了尽管存在显著的样本间序列变异，但仍存在保守的土壤类型特异性次生代谢物富集模式。这些数据用于创建环境中具有医学价值的天然产物生物地理分布图谱，这对于指导未来生物活性天然产物的发现应该是有用的。
