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

Abstract

Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well-known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seedborne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules, and could help improve land reclamation practices that involve alders.

Neighbours in nodules: the interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes of alder

“…or that they affect metal homeostasis in nitrogenfixing frankiae by facilitating, through metallophores, the acquisition of trace metals such as iron or molybdenum for use in nitrogenase (Deicke et al 2019). We have previously established that NFNE can synthesize siderophores in vitro (Garneau et al 2022) and Serratia (Ser83) isolates, with most of the Frankia biomass exhibiting compromised membrane integrity (Figure 5 -D, E, F). In many instances, inhibitory and neutral NFNE could be observed proliferating in coculture, most likely by using compromised Frankia biomass as the nitrogen source.…”

“…AvcI1. The isolates were routinely maintained on a unified endophyte medium (hereafter UEM), a complex, protein hydrolysate-rich medium (Garneau et al 2022). 24 NFNE were then selected for in vitro characterization and submitted to genomic sequencing along with frankiae including Frankia sp.…”

“…24 NFNE were then selected for in vitro characterization and submitted to genomic sequencing along with frankiae including Frankia sp. ACN10a (Garneau et al 2022). Table 1 presents the isolates, their identification based on 16S rRNA homology and their genome accession numbers.…”

“…Tryptophansupplemented ANEC30 was aged for the duration of the experiment and used to construct a 0 to 50 mg·L -1 IAA standard curve. Cocultures and controls were centrifuged and aseptically filtered after a 10-day static incubation at 30 °C and subjected to a modified Salkowski reagent assay, as previously described with 8 technical replicates per sample (Garneau et al 2022). Differences in auxin concentration were evaluated using Welch's t-test, by comparing the coculture supernatant with the corresponding NFNE-only culture supernatant.…”

“…rugosa) inoculated with environmental samples collected on and around a gold mine site in Northwestern Québec, Canada. We recently characterized their PGP traits and have sequenced their genomes (Garneau et al 2022). The present study aims to shed further light on the bacterial communities of alder nodules and more specifically, on the interactions they may have with frankiae, which are dominant in nodules.…”