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Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

机译：新型土壤细菌具有用于次级代谢产物生物合成的多种基因

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摘要

In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment(1,2). Most known antibiotics are derived from a few culturable microbial taxa(3), and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated(4). Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils(5-7), but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes(5). We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.
机译：在土壤生态系统中，微生物会产生多种次生代谢产物，例如抗生素，抗真菌剂和铁载体，介导与其他生物体和环境的交流，竞争和相互作用（1,2）。大多数已知的抗生素均来自少数可培养的微生物类群（3），并且很少研究土壤中绝大多数细菌的生物合成潜力（4）。在这里，我们从草地土壤基因组中重建了数百个近乎完整的基因组，并从先前研究不足的门上鉴定出了微生物，这些微生物编码了多种聚酮化合物和非核糖体肽生物合成基因簇，这些簇与经过深入研究的簇不同。这些生物合成基因座由新鉴定的酸性细菌，疣状疣和芽孢杆菌和候选门状杆菌编码。这些细菌群在土壤中高度丰富（5-7），但以前从未与遗传学上可靠地关联到次级代谢产物的产生。特别是在新发现的酸性细菌成员中鉴定了大量生物合成基因，该细菌是整个土壤生物群落中最丰富的细菌门（5）。我们从不同的谱系中鉴定出两个酸性细菌基因组，每个基因组编码一个异常大的生物合成基因库，每个基因组最多包含十五个大的聚酮化合物和非核糖体肽生物合成基因座。为了追踪我们研究的土壤生态系统中编码聚酮化合物合酶和非核糖体肽合成酶的基因的基因表达，我们在微观操作实验中采样了120个时间点，并使用元转录组学方法，发现基因簇在环境扰动下差异共表达。特定生物的转录共表达网络将生物合成基因与两组分系统，转录激活，推定的抗菌素耐药性和铁调节相关联，将代谢物的生物合成与环境感知和生态竞争过程联系起来。我们得出的结论是，以前已经低估了丰富的系统发育多样的土壤微生物的生物合成潜力。这些生物可能代表了天然产物的来源，可以满足对新抗生素和其他药物化合物的需求。

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  • 来源
    《Nature》 |2018年第7710期|440-444|共5页
  • 作者

    Crits-Christoph Alexander; Diamond Spencer; Butterfield Cristina N.; Thomas Brian C.; Banfield Jillian F.;

  • 作者单位

    Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA;

    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA;

    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA;

    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA;

    Univ Calif Berkeley, Innovat Genom Inst, Berkeley, CA 94720 USA;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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