Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA.
Department of Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA.
Nat Commun. 2023 Feb 23;14(1):1039. doi: 10.1038/s41467-023-36515-y.
Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.
了解植物和微生物之间的相互作用可以为微生物组管理提供信息，以提高作物生产力和对胁迫的恢复能力。在这里，我们应用基于基因组的方法来识别田间生长的柳枝稷和芒草的重复种植区中具有生态重要性的叶片微生物组成员，并在两个生长季节内定量分析柳枝稷的这些成员的活性。我们使用宏基因组和宏转录组测序，并整理了 40 个中高质量的宏基因组组装基因组（MAG）。我们发现，这些 MAG 所代表的类群（放线菌门、α-和γ-变形菌门以及拟杆菌门）在后期活跃，并上调了短链脱氢酶、钼喋呤氧化还原酶和聚酮合酶的转录物。大多数 MAG 表达与应激相关的途径，表明它们与宿主环境相互作用。我们还检测到季节性激活的萜类化合物和各种非核糖体肽途径的生物合成途径，这些途径的注释很差。我们的研究结果表明，与叶片相关的细菌种群具有季节性动态性，并对宿主信号有反应。
