Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
Microbiome. 2023 Sep 29;11(1):214. doi: 10.1186/s40168-023-01660-5.
Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed.
We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network.
The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.
植物有益细菌接种剂在农业中具有很大的吸引力，因为它们有可能促进植物的生长和健康。然而，根际微生物组的接种通常导致定植效果不理想或短暂，这是由于多种因素影响接种剂的命运。为了更好地了解植物有益接种剂在由数百种基因型和多因素选择机制组成的复杂根际微生物组中的命运，需要对具有高复杂性土壤微生物组的受控研究进行分析。
我们分析了在接种植物有益细菌恶臭假单胞菌（Pseudomonas protegens）后，在富含营养的指数增长和营养有限的稳定生长条件下（即生长和稳定群落，分别），丰富的自然土壤细菌群落的早期组成变化，分别在土壤或小麦根际环境中。恶臭假单胞菌在所有测试条件下均成功定植，并且在稳定群落的根际中更为丰富。养分可利用性是驱动微生物组组成、结构和潜在组装过程的主要因素。虽然对养分的利用导致了主要由同质选择组装的群落，但在营养缺乏条件下，随机过程占主导地位。我们还观察到在营养有限条件下根际选择效应增加，导致更多的扩增子序列变体（ASV）的相对丰度富集。恶臭假单胞菌的接种产生了离散的变化，其中一些涉及其他假单胞菌。假单胞菌菌株之间的直接竞争未能完全复制微生物组中的差异，并指出了更复杂的相互作用网络。
本研究结果表明，养分可利用性是土壤和小麦根际微生物组组成、结构和多样性的主要驱动力，并决定了控制早期微生物组发展的组装过程。接种剂的成功定植得益于小麦根际，并导致微生物组中其他成员发生离散变化。假单胞菌菌株之间的直接竞争仅部分解释了微生物组的变化，这表明根际或土壤界面的间接相互作用或空间分布可能对某些细菌的生存至关重要。视频摘要。
