Abstract
Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.
Highlights
Anthropogenic activities over the past decades, including pollution with heavy metals, pesticides and chemical fertilizer, as well as improper soil exploitation coupled with climate change have led to immense global soil degradation (Smith et al, 2016)
The second group harbors a mix of R. erythropolis and R. qingshengii strains
Average nucleotide identity (ANI) values between all analyzed R. erythropolis or R. qingshengii genomes were higher than 94% (Supplementary Figure 2)
Summary
Anthropogenic activities over the past decades, including pollution with heavy metals, pesticides and chemical fertilizer, as well as improper soil exploitation coupled with climate change have led to immense global soil degradation (Smith et al, 2016). The multifaceted interactions of plants and several plant-associated bacteria have been widely studied to understand the underlying molecular mechanisms and to exploit plant beneficial traits for sustainable agriculture (Berg et al, 2017; Rodriguez et al, 2019; Babin et al, 2021; Windisch et al, 2021) In this context it is important to further the knowledge of the functional repertoire of yet lesser known members of the plant microbiome such as Rhodococcus to understand what enables them to interact with the plant as well as other microbes and which traits could be useful for an application in demanding agricultural scenarios
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