framework 4.8 根证书_PNAS：被子植物根微生物组的装配和生态功能

1.摘要：

在植物和动物中，宿主相关的微生物群落在宿主营养，发育和免疫中起着基本作用。目前对影响宿主-微生物群落相互作用的因素了解甚少，但对于了解这些共共生体的进化和生态学却至关重要。植物根部在周围的土壤中形成两个不同的微生物区室：根际(根部周围的微生物)和内圈(根部内的微生物)。根系相关微生物是陆地植物进化的关键，是生态系统基本过程的基础。但是，目前尚不清楚植物进化如何影响根部微生物群落，进而了解这些微生物反过来影响如何影响植物生态系统，例如减轻生物和非生物胁迫源的能力。在这里，我们显示30个被子植物物种之间，在长达1.4亿年之久的变异中对根系细菌的多样性和组成影响。寄主之间根系微生物群落更显著的相似性会通过土壤反馈对植物生长产生负面影响，内圈和根际中的特定微生物分类可能会影响植物物种之间的竞争性相互作用。干旱改变了根微生物群落的组成，最明显的是增加了放线菌的相对丰度。然而，这种干旱反应在不同的寄主植物物种中是不同的，并且寄主特有的内圈链霉菌相对丰度的变化与寄主的耐旱性有关。我们的研究结果强调了根部微生物群变异的原因及其对植物响应生物和非生物胁迫的性能的生态重要性。

2.前言：

(1)在植物和动物中，相关的微生物群有助于宿主的营养，发育和免疫，但是如何扩展它们以影响宿主的生态功能和性能却鲜为人知。本文探讨宿主植物在宏观进化时间尺度上的进化如何塑造根系微生物群落的组成，以及根系微生物群落如何缓解宿主植物受到的生物和非生物环境胁迫。(2)目前对寄主植物物种间的变化如何影响内圈和根际微生物组成的理解仍然有限，加深这方面的研究对于理解根微生物群落如何影响其寄主植物的生态和性能至关重要。(3)土壤微生物长期以来被视为植物间相互竞争的关键，由这种“植物-土壤反馈”(PSF)介导的植物物种之间的竞争性相互作用会影响陆地生态系统的基本过程，比如群落组成和演替。但PSF的生物驱动因素尚未得到很好的了解，但很可能包括整个宿主植物物种中根系微生物群落的募集。(4)越来越多的证据表明，土壤微生物可能在植物抗旱性中起着重要的作用，但人们对其了解还很少。最近的工作表明，干旱还改变了许多草种中根系微生物群落的组成。然而，宿主植物根系微生物群多样性或组成的变化是否有助于植物抗旱性尚不清楚。(5)研究试图回答以下问题：(i)在30个系统发育上不同的寄主植物物种中，内圈和根际微生物群在多样性和组成上有何不同？(ii)寄主植物物种之间的进化差异会影响内圈和根际微生物组的组装吗？(iii)宿主植物物种之间根微生物组的变化是否会影响通过PSF的间接竞争相互作用？(iv)根微生物群落是否影响宿主植物的耐旱性？(6)作者的研究结果说明，寄主植物长时间内的进化如何影响根微生物组，以及根微生物群如何响应环境中生物和非生物成分的变化而影响植物的生长。

3.结果:

(1)寄主植物物种的内圈和根际微生物群的多样性和组成不同。(2)寄主植物物种之间的进化差异影响内圈和根际微生物组的组装。(3)寄主植物之间的根微生物群落的变化影响通过PSFs的间接竞争相互作用。(4)根微生物群落与宿主植物的耐旱性有关。

4.讨论：

我们证明了长时间内植物的进化会影响根微生物组的组装，进而影响宿主植物对生物和非生物环境胁迫的反应。我们的结果成功解决了我们的四个研究问题。首先，根微生物群的多样性和组成在整个寄主物种的内球和根际区室之间明显不同。其次，寄主植物物种解释了根微生物组多样性和组成的大部分变化。内球微生物组的变异表现出与潜在宿主植物系统发育的强烈对应关系，尽管根际并非如此。第三，内球和根际中宿主植物中根系微生物的募集模式通过PSF影响植物物种之间的间接竞争相互作用。第四，在干旱胁迫下，根内层动态响应，这些变化对应于寄主植物对干旱的耐受性变化。内圈和根际多样性和组成的巨大差异可能是植物的保守特征，反映了被子植物根部微生物群落组成的一般规则。植物物种在其内圈多样性和组成中的变化要比在其根际微生物群落中的变化大得多，这支持了寄主植物在内圈微生物群落组成中的重要性更高的观点。相比之下，尽管寄主植物物种对根际微生物群落有强烈影响，但根际组成与宿主植物的系统发育没有明确的关系。

Fig. 1. The diversity and composition of endosphere and rhizosphere compartments across plant species. (A) The endosphere exhibited less than one-quarter of the diversity found in the rhizosphere [F(1, 56) = 64.62 , PFDR < 0.001, P-value adjusted using the FDR]. (B) The abundance of bacterial phyla were significantly affected (GLM: PFDR < 0.05) by compartment (black star) and host plant species (green star, endosphere; yellow star, rhizosphere). (C) Endosphere diversity exhibited greater variation across host plants than rhizosphere diversity (χ2= 17.72, PFDR < 0.001). Endosphere diversity was also correlated with the underlying plant phylogeny, while rhizosphere diversity was not. (D) Plant species varied more in the composition of their endosphere versus rhizosphere compartments (χ2= 20.06, PFDR < 0.001). Mantel tests revealed a significant correlation between endosphere (but not rhizosphere) compositional similarity and phylogenetic relatedness.

寄主植物之间的PSF取决于根系菌群的总体组成差异；
      根系微生物可能通过土壤资源分配影响植物间的相互作用

Fig. 2. Root microbial composition is related to PSF. (A) PSF occurs when the soil microbes recruited by one plant influence the growth of other plants. Positive values indicate that a focal species performed better in soil conditioned by a heterospecific plant relative to a conspecific plant, whereas negative values indicate the opposite. (B) Plants exhibit enhanced growth when inoculated with soil conditioned by a heterospecific species with dissimilar endosphere (measured as weighted UniFrac distance) and (C) rhizosphere compartments (measured as unweighted UniFrac distance)寄主植物物种之间的PSF也取决于特定根细菌类群的差异丰度。这表明相互作用的宿主植物物种的根微生物群之间存在动态相互作用。

Fig. 3. Differential abundance of root bacterial taxa and PSF. Host plant species exhibit differential abundance for numerous root bacterial taxa in either the endosphere or rhizosphere, including: (A) an endosphere Streptomyces ASV and (B) the genus Pseudoxanthomonas, found in the rhizosphere (GLM: PFDR < 0.05). We estimated the log2 fold-change of differentially abundant root bacterial taxa among all unique pairs of focal (starred taxa on the host plant phylogeny) and soil-conditioning host plant species and correlated this with their measured PSF. Negative log2 fold-changes indicate a higher taxon abundance in soil-conditioning host plant species, while positive values indicate a higher taxon abundance in focal host plant species. (C) The differential abundance of the endosphere Streptomyces ASV between focal and soil-conditioning host plant species was positively related to their PSF. (D) However, the differential abundance of rhizosphere Pseudoxanthomonas between focal and soil-conditioning host plant species was negatively related to their PSF. (E and F) PSF between host plant species was significantly associated with the differential abundance of 66 endosphere taxa and 33 rhizosphere taxa. (E) In the endosphere, we observed a high proportion (35%) of PSF-related taxa exhibiting the association depicted in C (green lines illustrate significant trend lines between differential abundance of endosphere taxa and PSF at PFDR < 0.05). (F) While in the rhizosphere, a greater proportion (88%) of taxa exhibited the association depicted in D (yellow lines illustrate significant trend lines between rhizosphere taxa and PSF at PFDR < 0.05). See Dataset S2 for a full list of PSF-related taxa.干旱显著改变了根微生物组的组成，并略微降低了微生物多样性，对内圈的影响要大于根际微生物组。

Fig. 4. The effects of drought on root microbial communities. (A) The drought treatment (denoted by T) caused small reductions in the diversity of the endosphere and rhizosphere compartments (denoted by C), and (B) had large effects on the relative abundance of major bacterial phyla; starred phyla were significantly affected (GLM: PFDR < 0.05) by drought (green, endosphere; orange, rhizosphere). (C) Drought also had strong effects on the overall composition of the endosphere and rhizosphere microbiomes, although endosphere compartments exhibited a greater response. (Inset) Plants under drought experienced fourfold lower soil moisture than well-watered plants.内层放线菌(尤其是链霉菌科)的增加，与干旱耐受性的提高有关。

Fig. 5. The relationship between drought tolerance and Streptomycetaceae. (A) On average, the drought treatment (denoted by T) caused a 35% reduction in biomass compared with well-watered conditions [F(1, 44) = 17.37, P < 0.001], and plant species (denoted by S) varied significantly in their response to drought (represented by dots connected by individual lines). (B) Drought caused a sixfold increase in the mean relative abundance of endosphere Streptomycetaceae (Actinobacteria), but this effect varied among plant species. (C) Plant species with greater relative increases in an endosphere Streptomyces ASV under drought conditions had greater drought tolerance.

5.总结：

与寄主相关的微生物群对于植物和动物寄主的营养，发育和免疫力至关重要，但是我们对其更广泛的生态重要性的理解仍然有限。我们的研究提供了相关证据，证明了宿主微生物在多种宿主植物物种中发生变异的原因，以及这种变异对生物和非生物胁迫源的一般生态重要性。这项研究还可能为今后在不同农业系统中设计根系微生物群落以提高植物在竞争和干旱胁迫下的表现提供参考。