Oligotrophic Growth of Rhodococcus

Yoshida, Nobuyuki

doi:10.1007/978-3-030-11461-9_4

Cited by 4 publications

(2 citation statements)

References 39 publications

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“…These results suggest that this bacterium uses CO 2 as a carbon source for oligotrophic growth. However, the CO 2 fixation system has not been proven, and currently, its CO 2 requirement is not involved in the main carbon metabolism of N9T-4, while CO 2 incorporation has been confirmed in the cell components [5]. We suggest that alternative-specific carbon metabolism is involved in the oligotrophic growth of N9T-4.…”

Section: Introductionmentioning

confidence: 75%

“…Furthermore, DNA microarray analysis revealed that two genes, aldA and mnoA, encoding NAD-ALDH and NDMA-MDH, respectively, were strongly expressed under oligotrophic conditions [6]. All the super oligotrophs that we isolated previously belonged to the genera Rhodococcus and Streptomyces [1,5], and Nagata found that a transposon-induced mutant of Sphingobium japonicum UT26 showed oligotrophic features, and a Zn-dependent alcohol dehydrogenase was essential for oligotrophic growth [7].…”

Section: Introductionmentioning

confidence: 88%

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Oligotrophic Gene Expression in Rhodococcus erythropolis N9T-4 under Various Nutrient Conditions

et al. 2022

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Rhodococcus erythropolis N9T-4 is a super oligotroph that grows on an inorganic basal medium without any additional carbon and nitrogen sources and requires CO2 for its oligotrophic growth. Previously, we found that two genes, aldA and mnoA, encoding NAD-dependent aliphatic aldehyde dehydrogenase and N,N′-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase, respectively, were highly upregulated under oligotrophic conditions. In this study, we constructed reporter plasmids containing an enhanced green fluorescent protein gene under aldA or mnoA promoters (pAldA and pMnoA, respectively). Fluorescence analysis of N9T-4 cells with reporter plasmids revealed that tryptone and yeast extract strongly repressed the expression of oligotrophy-connected genes, whereas the effect of casamino acids was moderate. Furthermore, remarkably high expression of aldA and mnoA was observed when the reporter strains were grown in media containing primary alcohols, particularly ethanol. Malic acid repressed ethanol-induced gene expression, suggesting that C2 metabolism is involved in the oligotrophic growth of N9T-4. The regulation of oligotrophic gene expression elucidated in this study could provide appropriate conditions for the production of useful compounds in an oligotrophic microbial process.

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Section: Introductionmentioning

confidence: 75%

Section: Introductionmentioning

confidence: 88%

Oligotrophic Gene Expression in Rhodococcus erythropolis N9T-4 under Various Nutrient Conditions

et al. 2022

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Complete Genome Sequence of Rhodococcus qingshengii N9T-4

Obi

Moriuchi

Dohra

et al. 2022

Microbiol Resour Announc

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Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

Góngora,

Lirette,

Freyria

et al. 2024

Environmental Microbiome

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Background Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes. Results We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches. Conclusions Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines. Supplementary Information The online version contains supplementary material available at 10.1186/s40793-024-00616-y.

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Oligotrophic Growth of Rhodococcus

Cited by 4 publications

References 39 publications

Oligotrophic Gene Expression in Rhodococcus erythropolis N9T-4 under Various Nutrient Conditions

Oligotrophic Gene Expression in Rhodococcus erythropolis N9T-4 under Various Nutrient Conditions

Complete Genome Sequence of Rhodococcus qingshengii N9T-4

Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

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