Identification and Characterization of the Core Rice Seed Microbiome
Identification and Characterization of the Core Rice Seed Microbiome
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DOI：
10.1094/pbiomes-01-19-0009-r
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发表时间：
2019-01-01
影响因子：
4.4
通讯作者：
Dean, Ralph A.
中科院分区：
文献类型：
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作者：
Eyre, Alexander W.;Wang, Mengying;Dean, Ralph A.
在农业中使用微生物来提高作物产量是化学肥料和农药的新兴替代品;然而，它们的有效性往往受到宿主基因型和地理位置变化等因素的限制。为了解决这个问题，六种不同的水稻（Oryza sativa）种子的微生物组，来源于两个不同的基因型和两个收获年份的阿肯色州，美国的两个地点，进行了表征。使用高通量Illumine MiSeq测序在四个种子隔室（谷粒、外谷粒、外壳和外壳）中的每一个中鉴定细菌和真菌群落。对于真菌和细菌微生物组，在种子外壳中鉴定出更独特的扩增子序列变体，并且在谷物隔室中鉴定出最少的扩增子序列变体，然而，这仅导致真菌群落的多样性降低。主成分分析表明，每个组织室窝藏相对不同的细菌和真菌群落的三个最里面的车厢。鉴定了每个隔室的六种种子类型之间共享的细菌和真菌核心微生物组。所有隔室核心中的关键细菌属为鞘氨醇单胞菌属、甲基杆菌属和肠杆菌科中的分类群，据报道，其中的成员支持水稻生长。与细菌核心相比，鉴定出更多的真菌分类群，可能是由于过滤后更丰富的读数，鉴定出的关键属是链格孢属、汉那氏菌属和多孢目成员。这些核心成员代表了操纵水稻微生物组的有价值的候选者，减少了化学品的使用，同时提高了植物性能。
The use of microbes in agriculture for enhancing crop production is an emerging alternative to chemical fertilizers and pesticides; however, their effectiveness is often limited by factors such as host genotype and variability in geographic location. To address this issue, the microbiomes of six different rice (Oryza sativa) seeds, sourced from two locations in Arkansas, U.S.A. of two different genotypes and two harvest years, were characterized. The bacterial and fungal communities were identified in each of four seed compartments (grain, outer grain, husk, and outer husk) using high throughput Illumine MiSeq sequencing. More unique amplicon sequence variants were identified in the outer seed husk and least in the grain compartment for both the fungal and bacterial microbiomes, however this only resulted in a decrease in diversity for the fungal communities. Principal component analysis indicated that each tissue compartment harbored relatively distinct bacterial and fungal communities for the three innermost compartments. A bacterial and fungal core microbiome shared among the six seed types for each compartment was identified. Key bacterial genera in the core across all compartments were Sphingomonas, Methylobacterium, and taxa in the family Enterobacteriaceae, members of which have been reported to support rice growth. Compared with the bacterial core, more fungal taxa were identified, possibly resulting from the more abundant reads after filtering, and key genera identified were Alternaria, Hannaella, and members of the order Pleosporales. These core members represent valuable candidates for manipulating the rice microbiome, decreasing the use of chemicals while increasing plant performance.