Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment

Khilyas, Irina V.; Sorokina, Alyona V.; Markelova, Maria; Belenikin, M. S.; Shafigullina, Lilia; Tukhbatova, Rezeda I.; Shagimardanova, Elena; Blom, Jochen; Шарипова, М. Р.; Cohen, Michael F.

doi:10.1007/s00203-020-02057-w

Cited by 6 publications

(3 citation statements)

References 41 publications

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“…The first one includes sequences belonging to only R. erythopolis , the second includes R. qingshengii and R. erythropolis strains. Based on the clear separation we can confirm previous recommendations to separate the R. erythropolis clade into the two groups consisting of the species R. qingshengii and R. erythropolis respectively ( Sangal et al, 2016 ; Khilyas et al, 2020 ; Thompson et al, 2020 ). We also suggest that the R. erythropolis strains assigned to the R. qingshengii group should be re-named as previously recommended ( Sangal et al, 2016 ; Thompson et al, 2020 ).…”

Section: Discussionsupporting

confidence: 86%

“…Siderophores not only chelate iron and have beneficial effects in plant growth, they are also involved in bioremediation, function as biosensors and are relevant in microbial competition and defense against other microbes, which can lead to a beneficial biocontrol effect for the plant (Ahmed and Holmström, 2014;Gu et al, 2020;Pollak and Cordero, 2020). Genes involved in iron acquisition and siderophore production were identified in the RL1 genome, for example for the siderophore heterobactin, which is unique to the Rhodococcus genus (Carrano et al, 2001;Bosello et al, 2013;Khilyas et al, 2020). The in vitro assay for siderophore production was positive for RL1, corroborating that the identified genes were actually expressed.…”

Section: Rl1 Genome Reveals Successful Interaction and Survival Strategies In Association With Plantsmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Discussionsupporting

confidence: 86%

Section: Rl1 Genome Reveals Successful Interaction and Survival Strategies In Association With Plantsmentioning

confidence: 99%

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

et al. 2021

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“…We had no prior hypotheses for which species should particularly influence the relative performance of producers and non-producers, and future work would be needed to determine why these two species in particular had these effects. We note, however, that species of Rhodococcus [33] produces siderophores, allowing colonization of iron-poor rocky habitats [34]. We hypothesize that Rhodococcus might outcompete P. fluorescens non-producers for iron using siderophores that are not accessible for uptake by P. fluorescens non-producers.…”

Section: Discussionmentioning

confidence: 99%

Public goods exploitation is reduced in species-rich microbial communities

O’Brien

Culbert

Barraclough

2022

Preprint

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Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e. interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence select for increased intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2-15 species. We find, contrary to our prediction, that siderophore exploitation is reduced in high diversity communities, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. Our results suggest that maintaining a healthy soil microbiota could contribute to the maintenance of siderophore production in natural communities.

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Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment

et al. 2022

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Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment

Cited by 6 publications

References 41 publications

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

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

Public goods exploitation is reduced in species-rich microbial communities

Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment

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