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 extent 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 microbiomes for future agriculture and to develop effective bio-fertilizers.

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.)

“…On the other hand, the microbiota associated with adult plants is relatively more stable due to prior establishment of a more stable community likely with a higher and tighter degree of interactions 7 , 112 , 113 . LEfSe further corroborated these observations, identifying in young plants (tillering) almost twice of bacterial biomarker taxa than at other PGS (Figs.…”

“…At this PGS, flooding caused a significant increase (P < 0.05) in abundance of taxa associated with the genera Streptomyces , Massilia and Rheinheimera and a significant (P < 0.05) decrease in the proportion of Staphylococcus , Paracoccus and Micrococcus , which are bacterial endophytes that have been commonly isolated from wheat 114 and other plants 115 , 116 . Taxa affiliated to Massilia are frequently associated with wheat 7 , 117 and are considered putatively plant-beneficial due to their capability of producing proteases, sidephores and IAA 118 , 119 . We can speculate that their increase in leaf samples of flooding treatments at tillering might in our experiment had been leaf-mediated and buffered the plant physiological stress that has been induced by flooding.…”

“…Here, we performed a glasshouse experiment to investigate the response of the wheat bacterial leaf microbiota to flooding. Considering that (a) plant phenology is a major driver in shaping crop microbiota 7 , 41 , 42 and (b) the microbial response to abiotic stress depends largely on the plant developmental stage in which the stress occurs 43 , 44 , wheat plants were subjected to flooding either at tillering, booting and flowering. To monitor the effect of flooding on the leaf bacteria community assembly, we employed metabarcoding targeting the 16S rRNA gene.…”

Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota

“…Changes in belowground environments following flooding events are no less important than those that occur aboveground. Plant-associated microbiota plays a key role in fostering the host plant fitness (Turner et al, 2013;Compant et al, 2019), and it is well established that its composition is influenced by many host-associated and environmental factors (Francioli et al, 2016;Eisenhauer and Powell, 2017;Leff et al, 2018;Lewin et al, 2021). Recent research has demonstrated that alteration in soil moisture have significant effects on soil and root-associated microorganisms (Naylor and Coleman-Derr, 2018;Xu et al, 2018;Francioli et al, 2020).…”

Organic Connection of Holobiont Components and the Essential Roles of Core Microbes in the Holobiont Formation of Feral Brassica napus

“…Massilia is a well-known rhizospheric bacterium, which plays a key role in the succession of microbes in the early stages of the rhizosphere (Ofek et al, 2012). Massilia has also been identified as a network hub, and contributes to forming distinct microbiomes according to the host plants (Lewin et al, 2021). In this study, a phylogenic tree of the top 20 ASVs of Massilia indicated that distinct clusters of the dead leaf-or rhizosphere-related Massilia spp.…”