Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules

Abstract

Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

“…Root microbiome of C. myrtifolia contained Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes , and others, which is very similar to composition of Alnus glutinosa root microbiome ( Thiem et al, 2018 ), Casuarina glauca ( Ghodhbane-Gtari et al, 2021 ), several Legume roots ( Miranda-Sánchez et al, 2016 ; Xiao et al, 2017 ; Zgadzaj et al, 2016 ), and rice ( Edwards et al, 2015 ; Roman-Reyna et al, 2020 ).…”

“…It is commonly accepted that actinorhizal nodules are a special niche for symbiotic nitrogen fixation, which is primarily colonized by Frankia. However, as it has been shown by the culturedependent and -independent methods, several non-Frankia coexist with Frankia (Ghodhbane- Gtari et al, 2010bGtari et al, , 2021; Ghodhbane- Gtari and Tisa, 2014). At phylum level, the C. myrtifolia nodule microbiome differs from root only in term of relative abundance of each phylum and being composed of Bacteroidetes, Proteobacteria, and Actinobacteria.…”

Root Nodule Microsymbionts of Native Coriaria myrtifolia in Algeria

“…Recently other studies have confirmed this nodule surface emplacement of Casuarina incompatible Frankia strains. 35 , 36 …”

Deciphering the role of non-Frankia nodular endophytes in alder through in vitro and genomic characterization

“…It is difficult to assert the influence this may have had on results as little is known regarding the determinants of microbial diversity in nodules. In a study of Casuarina glauca nodules sourced in the natural environment, Ghodhbane-Gtari et al (2021) noted that water stress is one element that may have an impact on microbial diversity, specifically Frankia sp. sequence proportion in relation to total OTUs.…”