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Benning S, Pritsch K, Radl V, Siani R, Wang Z, Schloter M. (Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation. Microbiol Spectr 2024; 12:e0378323. [PMID: 38376357 PMCID: PMC10986565 DOI: 10.1128/spectrum.03783-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
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Affiliation(s)
- Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Zhongjie Wang
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University Munich, Munich, Germany
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Complete Genome Sequences of Two Rhodococcus sp. Strains with Large and Linear Chromosomes, Isolated from Apple Rhizosphere. Microbiol Resour Announc 2021; 10:e0015921. [PMID: 34137630 PMCID: PMC8210697 DOI: 10.1128/mra.00159-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Rhodococcus are usually able to catalyze a number of processes, which are of great interest for ecosystem performance as well as biotechnology. Here, we report the complete genome sequences of two Rhodococcus strains that were isolated from rhizosphere soil from an apple orchard in northern Germany.
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Thompson D, Cognat V, Goodfellow M, Koechler S, Heintz D, Carapito C, Van Dorsselaer A, Mahmoud H, Sangal V, Ismail W. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8. Front Microbiol 2020; 11:1417. [PMID: 32733398 PMCID: PMC7358434 DOI: 10.3389/fmicb.2020.01417] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/02/2020] [Indexed: 01/02/2023] Open
Abstract
Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.
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Affiliation(s)
- Dean Thompson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Huda Mahmoud
- Department of Biological Sciences, College of Science, Kuwait University, Safat, Kuwait
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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Francis IM, Vereecke D. Plant-Associated Rhodococcus Species, for Better and for Worse. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Hwang CY, Lee I, Cho Y, Lee YM, Baek K, Jung YJ, Yang YY, Lee T, Rhee TS, Lee HK. Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater. Int J Syst Evol Microbiol 2014; 65:465-471. [PMID: 25385992 DOI: 10.1099/ijs.0.070086-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped and non-motile strain, designated PAMC 27367(T), was isolated from rainwater collected on the Bering Sea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Rhodococcus. Phylogenetic analyses revealed that strain PAMC 27367(T) formed a robust clade with the type strains of Rhodococcus rhodnii, Rhodococcus aetherivorans and Rhodococcus ruber with 16S rRNA gene sequence similarities of 96.3 %, 95.8 % and 95.5 %, respectively. Cells of the strain grew optimally at 25 °C and at pH 6.5-7.0 in the presence of 0-2 % (w/v) sea salts. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and three unknown phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Cell wall analysis showed that strain PAMC 27367(T) contained meso-diaminopimelic acid. The genomic DNA G+C content was 77.1 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, we propose a novel species with the name Rhodococcus aerolatus sp. nov., with PAMC 27367(T) ( = KCTC 29240(T) = JCM 19485(T)) as the type strain.
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Affiliation(s)
- C Y Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - I Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Y Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Y M Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - K Baek
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Y-J Jung
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Y Y Yang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - T Lee
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Yongin-si, Gyeonggi-do 449-791, Republic of Korea
| | - T S Rhee
- Division of Polar Ocean Environment, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - H K Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
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Jaquet J, Weitzel P, Junge T, Schmidt B. Metabolic fate of the (14)C-labeled herbicide clodinafop-propargyl in soil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2014; 49:245-254. [PMID: 24502211 DOI: 10.1080/03601234.2014.868273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The metabolic fate of (14)C-phenyl-labeled herbicide clodinafop-propargyl (CfP) was studied for 28 days in lab assays using a soil from Germany (Ap horizon, silt loam, and cambisol). Mineralization amounted to 12.40% of applied (14)C after 28 days showing a distinct lag phase until day 7 of incubation. Portions of radioactivity extractable by means of 0.01 M CaCl2 solution (bioavailable fraction) decreased rapidly and were 4.41% after 28 days. Even immediately after application, only 57.31% were extracted with the aqueous solvent. Subsequent extraction using accelerated solvent extraction (ASE; acetonitrile/water 4:1, v/v) released 39.91% of applied (14)C with day 0 and 26.16% with day 28 of incubation from the samples. Non-extractable portions of radioactivity thus, increased with time amounting to 11.99% (day 0) and 65.00% (day 28). A remarkable increase was observed between 14 and 28 days correlating with the distinct increase of mineralization. No correlation was found throughout incubation with general microbial activity as determined by DMSO reduction. Analysis of the CaCl2 and ASE extracts by radio-TLC, radio-HPLC and GC/MS revealed that CfP was rapidly cleaved to free acid clodinafop (Cf), which was further (bio-) transformed; DT50 values (based on radio-TLC detection of the parent compound) were far below 1 day (CfP) and about 7 days (Cf). TLC analysis pointed to 2-(4-hydroxyphenoxy)-propionic acid as further metabolite. Due to fractionation of non-extractable residues, most of the (14)C was associated with fulvic and humic acids, portions in humin fractions and non-humics were moderate and low, respectively. Using a special strategy, which included pre-incubation of the soil with CfP and then mineralization of (14)C-CfP as criterion, a microorganism was isolated from the soil examined. The microorganism grew using CfP as sole carbon source with concomitant evolution of (14)CO2. The bacterium was characterized by growth on commonly used carbon sources and by 16S rDNA sequence analysis. The sequence exhibited high similarity with that of Rhodococcus wratislaviensis (99.56%; DSM 44107, NCIMB 13082).
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Affiliation(s)
- Jasmin Jaquet
- a Institute of Biology V (Environmental Research), RWTH Aachen University , Aachen , Germany
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Characterization and whole genome sequences of the Rhodococcus bacteriophages RGL3 and RER2. Arch Virol 2012; 158:601-9. [PMID: 23129131 DOI: 10.1007/s00705-012-1530-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
We report here the isolation and genome sequences of two novel phages, lytic for Rhodococcus and Nocardia species. Named RER2 and RGL3, both are members of the family Siphoviridae, and each possesses a novel genome of 46,586 bp and 48,072 bp, respectively. RER2 and RGL3 phages share a modular genome organization, as seen in other sequenced Siphoviridae phage genomes, and appear to share a common evolutionary origin. The genomes of these phages share no similarity with other Rhodococcus or Nocardia phages but are related to Mycobacterium phages. The data presented here extend our understanding of Rhodococcus phage genomics.
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