Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity

Abstract

Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.

Soil microbiome biomass, activity, composition and CO2 emissions in a long‐term organic and conventional farming systems

“…We, therefore, examined alpha and beta diversity and related indices comparing the two types of agricultural managements. The Venn diagram showed that a large proportion of bacteria was shared between the two managements and these might be considered a 'core microbiome' (Estendorfer et al, 2020) composed of poorly characterized microbes and presumably present in many soils, although not equally abundant. The presence of unique OTUs in ORG and CON samples may be due to selective soil properties deriving from different managements.…”

Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert

“…Although no driver OTUs or taxa were shared between the three vegetation belts, OTUs belonging to the order Rhizobiales, including members of the families Bradyrhizobiaceae and Hyphomicrobiaceae, displayed a high NESH score as potential driver taxa in the prepuna, puna, and steppe (Additional file 7 : Table S10). Genera of these families have been shown to contain soil microorganisms that can establish beneficial relationships with plant roots by fixing nitrogen [ 81 , 82 ], including OTUs belonging to Bosea [ 83 ], Bradyrhizobium [ 84 , 85 ] and Rhodoplanes [ 86 ]. Taxa and specific OTUs known to include species relevant for plant protection were also identified as potential drivers of the transition between the BS to the RSS compartment, particularly in the puna and steppe.…”

Plant–Soil Interactions as Drivers of the Structure and Functions of Plant Communities

“…Soil factor effects on plant community structure are addressed by highlighting plant trait selection by degraded habitats in ultramafic soils for mine reclamation [3], by specifying the effect of microorganism supply (AMF, Frankia and Rhizophagus fasciculatus) on plant community structures and ecological restoration [4], and by reviewing the role of Arbuscular Mycorrhizal Fungi (AMF) to cope with biotic and abiotic stresses and improve plant growth [5]. In addition, a distinct composition of plant-associated core bacterial communities independent of land use intensity is identified [6].…”