Hartman Kyle, Schmid Marc W, Bodenhausen Natacha, Bender S Franz, Valzano-Held Alain Y, Schlaeppi Klaus, van der Heijden Marcel G A
Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
MWSchmid GmbH, Glarus, 8750, Switzerland.
Environ Microbiome. 2023 Jul 31;18(1):65. doi: 10.1186/s40793-023-00521-w.
A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure.
We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts.
Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome - which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.
植物微生物组研究的一个主要目标是确定与植物相关的微生物群落的驱动因素。虽然土壤特性和宿主植物身份是根微生物组组成的关键驱动因素，但重要的植物根共生体的存在与否是否也决定了整体微生物组组成仍未得到解决。丛枝菌根真菌（AMF）和固氮根瘤菌是广泛存在的有益根共生体，它们能显著增强植物营养、植物健康和根系结构。因此，我们假设共生体类型决定了根微生物组结构。
我们在温室中种植了来自五个科的17种植物，它们的共生关系不同（无共生关系、仅AMF、仅根瘤菌或AMF和根瘤菌），并使用细菌和真菌扩增子测序来表征它们的根微生物组。虽然植物系统发育和物种身份是决定根微生物组组成的最重要因素，但我们发现共生关系类型也是多样性和群落组成的一个重要驱动因素。我们发现包括酸杆菌门、衣原体门、厚壁菌门和疣微菌门成员在内的细菌门对AMF和根瘤菌的存在与否有一致的反应，并确定了在不同共生组中特异性富集的OTU群落。分别有80、75和57个细菌OTU对无共生关系的植物物种、与AMF形成共生关系的植物物种或与AMF和根瘤菌都形成共生关系的植物物种具有特异性。同样，9、14和4个真菌OTU对这些植物共生体组具有特异性。重要的是，在没有主要共生体的情况下，微生物群落组成中的这些一般共生足迹也很明显。
我们的结果表明，宿主植物的共生关系在更广泛的根微生物组上留下了印记——我们称之为共生型。这些发现表明存在一种根微生物组的基本组装原则，该原则取决于宿主植物的共生关系。
