Crop Host Signatures Reflected by Co-association Patterns of Keystone Bacteria in the Rhizosphere Microbiota

Abstract

Background: The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. Results: Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extend of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. Conclusions: Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiome for future agriculture and to develop effective bio-fertilizers.

A multi-omics approach to unravel the interaction between heat and drought stress in the Arabidopsis thaliana holobiont

“…Indeed, the root and rhizosphere communities undergo an initial period of dynamic recruitment followed by a later period of relative stability. The roots grown under pre-flowering drought treatment showed a more pronounced reshape of microbiota than post-flowering drought treatments (Xu et al 2018;Francioliet al 2021;Lewin et al 2021;Francioli et al2022). While confirming the orchestrated response of the whole holobiont to a combination of abiotic stressors, based on the studies mentioned above and our work, it would be very promising to investigate dynamics occurring as a function of plant stage at root and rhizosphere microbiota level.…”

“…This active recruitment of microorganisms improves resilience to abiotic stresses by eliciting physiological, biochemical, and molecular responses in the plant's local and distal parts (Meena et al 2017) (Saeed et al 2021). Noteworthy, single and combined abiotic stresses may indirectly alter plant functions via the modulation of plant-and root-associated microbiota (Rahman, Hamid & Nadarajah 2021), triggering substantial changes in plant development (Francioli et al 2021;Lewin, Francioli, Ulrich & Kolb 2021). Despite plant adaptation processes and the microbiota responses to abiotic stresses being known, the effect of combined stressors on holobionts is still poorly investigated (Rivero, Mittler, Blumwald & Zandalinas 2022).…”