Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant–Microbe Interaction Traits

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.

Physiological and biochemical characterization and genome analysis of Rhodococcus qingshengii strain 7B capable of crude oil degradation and plant stimulation

“…For this work, several strains of R. qingshengii were sequenced and assembled ( Table 3 ). Previously, strain X5 [44] was identified as R. erythropolis . However, in accordance with the classification proposed in the article [45] , later we redefined it as R. qingshengii .…”

Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana

“…In the experiments conducted in the study, the following bacterial strains were used as control or as plant pathogenic strains: the strain Bacillus velezensis FZB42 DSM 23117, producing antifungal compounds like surfactin, fengycin, and iturin (Chowdhury et al, 2015 ), the IAA-producing Herbaspirillum frisingense GSF30 DSM 1328 (Kirchhof et al, 2001 ), the siderophore-producing Rhodococcus qingshengii RL1 (Kuhl et al, 2021 ), the AHL biosensor strain Agrobacterium tumefaciens A136 ATCC 51350 (Han et al, 2016 ), the AHL-producer strain Acidovorax radicis N35 DSM 23535 (Li D. et al, 2011 ), the biofilm-producing Pseudomonas simiae WCS417r (Pieterse et al, 2020 ), and the non-biofilm-producing Escherichia coli DH5α (Anton and Raleigh, 2016 ). Plant-pathogenic strains were Xanthomonas translucens (Sapkota et al, 2020 ) and Pseudomonas syringae DC3000 ( Pst DC3000) (Xin and He, 2013 ).…”

“…Determination of IAA production was performed according to the method of Gordon and Weber ( 1951 ), as described in Kuhl et al ( 2021 ), with modifications. A pre-grown liquid culture of SCA7 was transferred to a fresh NB medium supplemented with 5 mM tryptophan (1 mg/ml, Sigma) and grown for 24 h. Afterward, liquid cultures were centrifuged, and the collected supernatant was mixed in equal volumes (100 μL) with Salkowski reagent [0.01 M FeCl3 anhydrous (Fluka Biochemika) in perchloric acid (HClO4) 35% (Merck)] (Loper and Schroth, 1986 ) and 1 μL of orthophosphoric acid (Sigma).…”

“…Analysis of siderophore production was performed following the protocols of Pérez-Miranda et al ( 2007 ) and Lynne et al ( 2011 ), with modifications as described in Kuhl et al ( 2021 ). Briefly, 25 μL of an SCA7 overnight-grown culture was pipetted on NB agar plates and incubated for 48 h. Dye solutions [chrome azurol blue S (Sigma), FeCl3 (Fluka Biochemika) and HDTMA (Hexadecyltrimethylammonium bromide, Sigma)] were prepared and mixed according to Lynne et al ( 2011 ).…”

“…Analysis of siderophore production was performed following the protocols of Pérez-Miranda et al (2007) and Lynne et al (2011), with modifications as described in Kuhl et al (2021).…”