Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants.
Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants.
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DOI：
10.1128/msystems.01125-21
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发表时间：
2021-12-21
期刊：
影响因子：
6.4
通讯作者：
Des Marais DL
中科院分区：
文献类型：
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作者：
Mueller UG;Juenger TE;Kardish MR;Carlson AL;Burns KM;Edwards JA;Smith CC;Fang CC;Des Marais DL
我们开发了一种人工选择根际微生物群落的方法，赋予在钠盐胁迫或铝盐胁迫下生长的模式草Brachypodium disachyon耐盐性。在受控的温室环境中，我们在没有进化、高度近亲繁殖的植物群体中以差异方式繁殖根际微生物群落；因此，在我们的实验中，只有微生物群落进化，但植物并没有并行进化。为了在植物之间移植微生物组时最大限度地保持微生物组的永久化，从而最大限度地响应微生物组选择，我们改进了早期的方法，方法包括：(I)在每个选择周期开始时接种种子时控制微生物组的组装；(Ii)在植物之间转移之前对微生物组分进行分离，以仅对细菌和病毒微生物组分进行选择；(Iii)随着每个选择周期的进行，盐胁迫逐渐从轻微盐胁迫增加到极端盐胁迫，以最大限度地减少植物过度胁迫的机会；(Iv)使用两种非选择控制处理(例如非选择微生物富集法和无效接种法)，使之能够与所选择的微生物组赋予植物的改善适应性益处进行比较。与以前的方法不同，我们的选择协议产生的微生物群只需1到3轮微生物组选择就能增强植物的适应性。经过9轮微生物组筛选，筛选出的耐铝盐微生物群的作用是非特异性的(这些人工选择的微生物群同样改善了钠盐胁迫和铝盐胁迫)，但选择的赋予钠盐胁迫耐性的微生物群的效果是特定的(这些人工选择的微生物群不赋予铝盐胁迫的耐受性)。人工选择微生物群落的植物比未选择对照微生物群落的植物种子产量高55%至205%。重要性我们开发了一种实验方案，改进了早期对微生物群进行人工选择的方法，然后测试了我们方案在培育赋予植物耐盐性的根相关细菌微生物群方面的有效性。盐胁迫限制了作物的生长和种子产量，而人工选择的具有耐盐性的微生物群最终可能有助于提高农业生产率。与以前的微生物组选择实验不同，我们的选择方案只对与根相关的微生物组进行了1到3轮的人工选择就产生了提高植物生产力的微生物组，在9轮微生物组选择后，极端盐胁迫下的种子产量提高了55%到205%。虽然我们在受控温室条件下人工选择微生物群，但与传统植物育种相比，在极端盐胁迫下将种子产量提高55%至205%是对植物生产力的显著提高。我们描述了一系列额外的实验方案，这些方案将促进对决定微生物组选择的有效性和响应的关键参数的深入了解。
We develop a method to artificially select for rhizosphere microbiomes that confer salt tolerance to the model grass Brachypodium distachyon grown under sodium salt stress or aluminum salt stress. In a controlled greenhouse environment, we differentially propagated rhizosphere microbiomes between plants of a nonevolving, highly inbred plant population; therefore, only microbiomes evolved in our experiment, but the plants did not evolve in parallel. To maximize microbiome perpetuation when transplanting microbiomes between plants and, thus, maximize response to microbiome selection, we improved earlier methods by (i) controlling microbiome assembly when inoculating seeds at the beginning of each selection cycle; (ii) fractionating microbiomes before transfer between plants to harvest, perpetuate, and select on only bacterial and viral microbiome components; (iii) ramping of salt stress gradually from minor to extreme salt stress with each selection cycle to minimize the chance of overstressing plants; (iv) using two nonselection control treatments (e.g., nonselection microbial enrichment and null inoculation) that permit comparison to the improving fitness benefits that selected microbiomes impart on plants. Unlike previous methods, our selection protocol generated microbiomes that enhance plant fitness after only 1 to 3 rounds of microbiome selection. After nine rounds of microbiome selection, the effect of microbiomes selected to confer tolerance to aluminum salt stress was nonspecific (these artificially selected microbiomes equally ameliorate sodium and aluminum salt stresses), but the effect of microbiomes selected to confer tolerance to sodium salt stress was specific (these artificially selected microbiomes do not confer tolerance to aluminum salt stress). Plants with artificially selected microbiomes had 55 to 205% greater seed production than plants with unselected control microbiomes. IMPORTANCE We developed an experimental protocol that improves earlier methods of artificial selection on microbiomes and then tested the efficacy of our protocol to breed root-associated bacterial microbiomes that confer salt tolerance to a plant. Salt stress limits growth and seed production of crop plants, and artificially selected microbiomes conferring salt tolerance may ultimately help improve agricultural productivity. Unlike previous experiments of microbiome selection, our selection protocol generated microbiomes that enhance plant productivity after only 1 to 3 rounds of artificial selection on root-associated microbiomes, increasing seed production under extreme salt stress by 55 to 205% after nine rounds of microbiome selection. Although we artificially selected microbiomes under controlled greenhouse conditions that differ from outdoor conditions, increasing seed production by 55 to 205% under extreme salt stress is a remarkable enhancement of plant productivity compared to traditional plant breeding. We describe a series of additional experimental protocols that will advance insights into key parameters that determine efficacy and response to microbiome selection.