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            Genome Assembly of a Plant-Associated Rhodococcus qingshengii Strain (RL1) Isolated from Eruca sativa Mill. and Showing Plant Growth-Promoting Properties

Kuhl, Theresa; Felder, Marius; Nußbaumer, Thomas; Fischer, Doreen; Kublik, Susanne; Chowdhury, Soumitra Paul; Schloter, Michael; Rothballer, Michael

doi:10.1128/mra.01106-19

Cited by 5 publications

(6 citation statements)

References 12 publications

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“…MS6 is similar to auxin it induces cell wall formation and promotes the growth of basal stem cells. Many other studies also have shown that Rhodobacteraceae promote plant growth (Stevens et al, 2017;Abraham and Silambarasan, 2018;Kuhl et al, 2019;Vergani et al, 2019). Ambient environmental parameters are another important factor affecting the abundance and diversity of microbial community on the surface of U. fasciata.…”

Section: Discussionmentioning

confidence: 96%

Hyunsoonleella sp. HU1-3 Increased the Biomass of Ulva fasciata

et al. 2022

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Green algae are photosynthetic organisms and play an important role in coastal environment. The microbial community on the surface of green algae has an effect on the health and nutrition of the host. However, few species of epiphytic microbiota have been reported to play a role in promoting the growth of algae. In this study, 16S rDNA sequencing was used to study the changes of microbial composition on the surface of Ulva fasciata at different growth stages. Some growth promoting bacteria were identified. The possible growth-promoting behavior of the strains were verified by co-culture of pure bacteria obtained from the surface of U. fasciata with its sterile host. Among the identified species, a new bacterial species, Hyunsoonleella sp. HU1-3 (belonging to the family Flavobacteriaceae) significantly promoted the growth of U. fasciata. The results also showed that there were many genes involved in the synthesis of growth hormone and cytokinin in the genome of Hyunsoonleella sp. HU1-3. This study identified the bacterium Hyunsoonleella sp. HU1-3 for the first time, in which this bacterium has strong growth-promoting effects on U. fasciata. Our findings not only provide insights on the establishment of the surface microbiota of U. fasciata, but also indicate that Hyunsoonleella sp. HU1-3 is one of the important species to promote the growth of U. fasciata.

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Section: Discussionmentioning

confidence: 96%

Hyunsoonleella sp. HU1-3 Increased the Biomass of Ulva fasciata

et al. 2022

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“…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 ). The genomes of RL1 and djl6 were clearly identified as belonging to the R. qingshengii cluster ( Xu et al, 2007 ; Kuhl et al, 2019 ) and had more genes in common with each other than with BG43 ( Figure 2 ), whereas the BG43 genome was classified as R. erythropolis ( Müller et al, 2014 ; Rückert et al, 2015 ). Despite the clear separation the strains RL1 and BG43 had many functional traits in common, indicating a close functional overlap between the species.…”

Section: Discussionmentioning

confidence: 99%

“…The genome of Rhodococcus qingshengii RL1 ( Kuhl et al, 2019 ) was compared to the genomes of the type strain Rhodococcus qingshengii djl6 ( Xu et al, 2007 ; Wang et al, 2010 ; Táncsics et al, 2014 ), as well as the closely related soil isolate Rhodococcus erythropolis BG43 ( Rückert et al, 2015 ). The genome djl6 is based on the species R. jialingiae ( Wang et al, 2010 ) which was later identified as a synonym of the type strain R. qingshengii ( Táncsics et al, 2014 ).…”

Section: Methodsmentioning

confidence: 99%

“…The genome annotation of RL1 revealed several genes which have been previously identified to be involved in stress tolerance under different abiotic stress conditions, bioremediation of toxic compounds, rhizosphere colonization and (beneficial) plant-microbe interactions and were partly verified by manual annotation with blastp alignment (Supplementary Table 4). In more details, the RL1 genome harbors many genes, which References Kuhl et al, 2019Xu et al, 2007Wang et al, 2010;Táncsics et al, 2014Rückert et al, 2015 can be expressed to withstand osmotic, salt, oxidative and acidic stress and are relevant for heavy metal tolerance (mercury, lead, cadmium, arsenic) and bioremediation of aromatic hydrocarbons (alkB, catA) and fossil fuels (dszB). Moreover, genes potentially involved in multiple drug resistance, DNA repair by phosphorothioation, antibiotic resistance and degradation of CO and hydrogen could be identified, for example the complete carbon monoxide dehydrogenase (CODH) and a [NiFe]-hydrogenase cluster.…”

Section: Functional Annotation Of Rl1 Genomementioning

confidence: 99%

“…The here studied closely plant associated Rhodococcus qingshengii RL1 was isolated from surface sterilized Rucola ( Eruca sativa L.) leaves and the genome was recently sequenced ( Kuhl et al, 2019 ). The type strain of species R. qingshengii djl-6 was isolated from a carbendazim polluted soil ( Xu et al, 2007 ).…”

Section: Introductionmentioning

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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