Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon. Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not. The consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

中文翻译：

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土壤、衰老和分泌物利用：Paragon 变种的特征。春季面包小麦根部微生物组

传统的农业害虫防治和作物施肥方法是不可持续的。为了满足不断增长的需求，我们必须找到对生态负责的方法来控制疾病和提高作物产量。与根部相关的微生物组可以帮助植物抑制疾病、缓解非生物胁迫和提高营养物质的生物利用度。目前工作的目的是描绘不同条件下与小麦根际和根内圈相关的细菌、真菌和古细菌群落。我们还旨在使用 13CO2 稳定同位素探测 (SIP) 来识别根室内能够利用宿主来源的碳的微生物。元条形码显示，不同区室中细菌、真菌和古细菌的群落组成发生了显着变化。这种转变对于细菌和真菌最为明显，而我们观察到以氨氧化古菌为主的古菌群落的选择较弱。在多种土壤类型中，我们发现土壤接种物是内圈群落组成的重要驱动因素，然而，一些细菌家族被确定为所有土壤条件下的核心富集类群。其中最丰富的是链霉菌科和伯克霍尔德杆菌科。此外，随着植物衰老，两个科的丰度都减少，这表明需要来自活植物的输入来维持它们在内层的丰度。稳定同位素探测表明，伯克霍尔德氏菌科内的细菌类群以及其他核心富集类群（例如假单胞菌科）能够利用根分泌物，但链霉菌科则不能。链霉菌科和伯克霍尔德氏菌科在内圈内的持续富集，以及发育衰老后丰度的减少，表明这些科在小麦根微生物组中发挥着重要作用。虽然链霉菌科不利用根际的根系分泌物，但我们提供的证据表明，假单胞菌科和伯克霍尔德氏菌科类群是通过根系分泌物招募到小麦根部群落的。这种对作物微生物组形成的更深入了解将使研究人员能够进一步表征这些相互作用，并可能有助于未来提高产量和生物防治的生态负责任的方法。