Biology subjects

Blahovska, Z.

Publications and source records attributed to Blahovska, Z..

4 recordsLinked to original sources

bioRxiv2026

Identification of Potential Regulatory Non-Coding RNAs in Lotus Japonicus Symbiosis

O_LISymbiosis between legumes and rhizobia is beneficial on nutrient-poor soils, as it enables the fixation of atmospheric N2. To establish this symbiosis, gene expression in both the host plant and the symbiont has to be regulated. To understand the underlying RNA-mediated regulation of host gene expression, we designed experiments to identify competing endogenous networks involving circular RNA, microRNA, and linear transcripts during symbiosis, using wt and symbiosis-deficient Lotus japonicus mutants with the rhizobium Mesorhizobium loti (M. loti). C_LIO_LICircRNA, miRNA, and linear transcripts were identified from Lotus japonicus wildtype and CCamK mutant (ccamk-13; snf-1) seedlings without inoculation or with M. loti inoculation using deep short-read sequencing with rRNA-depletion and random primers. C_LIO_LIDifferentially expressed miRNAs showed negative correlations to predicted target genes and may regulate symbiotic processes. The symbiosis essential iron-sensor LjnsRING/BRUTUS expresses a circRNA which was upregulated in symbiotic treatments. This circRNA may act as a target mimic and contribute to nodule longevity. CircRNAs are predicted to act predominantly as trans-regulatory molecules with similar frequencies in Arabidopsis thaliania, Oryza sativa, and Lotus japonicus. C_LIO_LIWe identified novel miRNAs, long noncoding RNAs, and circRNAs, and nominated several as potential new regulatory non-coding RNAs that may act as target mimics to stabilize genes and support symbiosis. C_LI SummarySymbiosis between Lotus japonicus and Mesorhizobium loti involves treatment-specific regulation of competing endogenous RNA networks involving circular RNA, miRNA, and linear transcripts.

plant biology↗

bioRxiv2026

The common symbiosis pathway controls plant root microbiomes in a host-specific manner

Crop nutrition depends on plant-microbe interactions, yet it remains unclear whether conserved genetic pathways impose universal rules on root microbiome assembly across plant hosts. Here, we show that the Common Symbiosis Signalling Pathway (CSSP), a conserved genetic module controlling endosymbiosis with arbuscular mycorrhizal fungi and nitrogen-fixing bacteria, regulates root microbiome assembly in a host-specific manner across contrasting fertilisation regimes. Using Lotus japonicus and Hordeum vulgare, we demonstrate that mutations in orthologous CSSP genes remodel root bacterial communities in both species, but with distinct taxonomic outcomes. In Lotus, CSSP disruption reduces rhizobial colonisation and promotes niche replacement by commensal taxa, whereas in Hordeum, the same mutations broadly restructure bacterial lineages without converging on Lotus-like responses. Root exudate profiling reveals host-specific metabolic differences, particularly in phenylpropanoid (flavonoids and coumarins) and gibberellin pathways, linking CSSP activity to chemically distinct rhizosphere environments that correlate with divergent microbiome assembly patterns across hosts. Moreover, root bacterial community composition accurately predicts plant nutritional status, highlighting tight coupling between host physiology and microbiome composition. Together, our results show that conserved symbiosis signalling regulates root microbiome assembly, while host-specific metabolic environments determine taxonomic outcomes. This extends CSSP function beyond canonical endosymbioses and positions symbiosis signalling as a general determinant of plant-microbiome interactions with implications for crop nutrition. Significance StatementRoot microbiomes influence plant nutrition, yet how conserved host genetic pathways controlling interactions with intracellular symbionts shape root-associated microbiome assembly across divergent plant species remains unresolved. The Common Symbiosis Signalling Pathway (CSSP), conserved across most land plants, regulates root microbiome composition in both a legume and a cereal, but with distinct taxonomic outcomes. These effects correlate with CSSP-dependent differences in root exudate chemistry and host metabolic profiles. Together, our results show that conserved symbiosis signalling operates within host-specific metabolic contexts, providing a framework for understanding why disruption of the same genetic pathway can lead to divergent microbiome configurations across plant species.

plant biology↗

bioRxiv2024

Functional capacities drive recruitment of bacteria into plant root microbiota

Host-associated microbiota follow predictable assembly patterns but show significant variation at the bacterial isolate level depending on the host and environmental context. This variability poses challenges for studying, predicting, and engineering microbiomes. Here we examined how Arabidopsis, Barley, and Lotus plants recruit specific bacteria from highly complex synthetic communities (SynComs) composed of hundreds of bacterial isolates originating from these plants when grown in natural soil. We discovered that, despite their taxonomic diversity, bacteria enriched by these three plant species encode largely overlapping functions. A set of 266 functions common among all host-associated communities was identified at the foundation of the microbiotas functional potential. Analysis of the differences observed between root-associated communities revealed that functions recruited by Arabidopsis and Barley were primarily driven by the SynCom composition, while Lotus selected fewer isolates but with more diverse functionalities, akin to a Swiss army knife strategy. We analysed the variation at the functional level and found this can be explained by the combined functions of bacteria at the family level. Additionally, across major taxa, the isolates covering a broader range of their familys functional diversity achieved higher relative abundance in the root communities. Our work sheds light on key functions and principles guiding the recruitment of bacterial isolates into root microbiota, offering valuable insights for microbiome engineering and inoculant discovery at a previously inaccessible taxonomic level.

plant biology↗

bioRxiv2023

Nitrogen source and Nod factor signaling map out the assemblies of Lotus japonicus root bacterial communities

Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is not known how this process takes place and whether it is independent of nitrogen nutrition. We use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We found that Nod factors are produced by symbionts to activate Nod factor signaling in the host, and this modulates the assembly of a symbiotic root microbiota. Lotus plants grown in symbiosis-permissive or suppressive soils delineated three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We found that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrated that selected bacterial genera delineating state-dependent microbiomes have a high level of accurate prediction.

plant biology↗