Complete Genome Sequences of Four
            <i>Microbacterium</i>
            Strains Isolated from Metal- and Radionuclide-Rich Soils

Ortet, Philippe; Gallois, Nicolas; Long, Justine; Zirah, Séverine; Berthomieu, Catherine; Armengaud, Jean; Alpha-Bazin, Béatrice; Barakat, Mohamed; Chapon, Virginie

doi:10.1128/mra.00846-19

Cited by 5 publications

(4 citation statements)

References 17 publications

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“…Moreover, 3 rRNA and 53 tRNA were also detected by DFAST. The GC content of the bacterial genome was 69.90%, which corroborated with the fact of Microbacterium paraoxydans as a high GC content organism (Table 5) (Ortet et al, 2019). Both the server Prokka and DFAST failed to detect any CRISPR sequence in the genome (Table 5&6).…”

Section: Genome Assembly and Metagenomic Classi Cation Of The Isolate...supporting

confidence: 65%

Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – a heavy metal hypertolerant and plant growth promoting bacterium

Mandal,

Das,

Adhikari

et al. 2024

Preprint

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A heavy metal hypertolerant plant growth promoting bacterium was isolated from arsenic contaminated garden soil of Bhagobangola I block (Murshidabad district). Metagenomic classification identified the bacterial isolate as a member of genus Microbacterium. Taxonomic assessment showed maximum average nucleotide identity (89.99%) with Microbacterium paraoxydans strain DSM 15019. Prokaryotic genome annotation was performed by Prokka, DFAST and RAST. The entire genome consisted of 3365911 bases with 69.90% GC-content. Prokka detected 3216 coding sequences (1461 hypothetical sequences), 3283 genes, 10 miscellaneous RNA, 3 rRNA, 53 tRNA and 1 tmRNA. DFAST detected 3257 coding sequences (1217 hypothetical sequences), 3 rRNA and 53 tRNA. Both Prokka and DFAST failed to detect any CRISPR sequence. RAST could detect 3285 coding sequences and 49 RNAs in the genome. Only 25% (821) of these sequences fell within the subsystem of RAST, which included 789 coding sequences as non-hypothetical and 32 sequences as hypothetical. Genes and Gene clusters responsible for arsenic resistance (arsR, arsB, arsC, acr1, acr2, acr3), other heavy metal (Copper, Manganese, Zinc, etc.) tolerance and plant growth promotion (Auxin biosynthesis, Siderophore mediated iron acquisition, Phosphate and polyphosphate metabolism, Trehalose biosynthesis, etc.) could also be identified in the Microbacterium paraoxydans genome. The heavy metal (arsenic) hypertolerance, bioremediation potential and plant growth promoting nature of the bacterium were confirmed by plate assay, SDDC assay and pot experiments, respectively. The aforementioned traits point towards the probable application of the bacterium as a bioremediation tool and biofertilizer, for reduction of arsenic toxicity and promotion of plant growth.

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Section: Genome Assembly and Metagenomic Classi Cation Of The Isolate...supporting

confidence: 65%

Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – a heavy metal hypertolerant and plant growth promoting bacterium

Mandal,

Das,

Adhikari

et al. 2024

Preprint

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“…Using proteogenomics, we further showed the high impact of uranyl on the proteome of this strain (45,46). In the present work, we have examined three additional Microbacterium strains for which we obtained the whole-genome (47), and subjected them to comparative analysis (Fig. 1a).…”

Section: Introductionmentioning

confidence: 91%

“…Peptides obtained after in-gel proteolysis of proteins with trypsin were characterized using a Q-Exactive HF mass spectrometer (ThermoFisher) coupled to an UltiMate 3 000 LC system (Dionex-LCPackings) operated according to a Top20 data-dependent acquisition method, as previously described (48). Data were interpreted as described in (46) against the genome-annotated protein sequence databases of the four Microbacterium strains (47). The statistical protein abundance variations between the exposure conditions were compared using the T-Fold option of the PatternLab 2.0 software (49), taking into account the four replicates.…”

Section: Shotgun Proteomic Analysismentioning

confidence: 99%

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

et al. 2021

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Author Contributions: V.C. designed and supervised the study. V.C. and L.P. performed the uranium exposure experiments and prepared the samples for proteomics. N.T., M.F. and L.F. performed microscopic analysis and ICP-AES measurements. B.A.-B. acquired the proteomics data and N.G., B.A.-B. and J.A. performed the proteomic analyses. P.O. and M.B. performed genomic and phylogenetic analyses and constructed ORF databases for proteomics. A.M.A. established UipA topology in vivo. N.G. purified the recombinant proteins and performed fluorescence titration experiments, assisted by N.B. N.G. and D.L. performed native mass spectrometry experiments. N.G. acquired FTIR data under C.B. supervision. N.G. prepared the samples for synchrotron-based analysis and participated in EXAFS data acquisition. C.D.A. performed EXAFS data acquisition and processing. N.B. and N.G. performed crystallization tests and obtained the protein crystals under supervision of P.A. P.A. and P.L. resolved the

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“…Many Microbacterium spp. have been study due to their biotechnological interest in facilitating bioremediation (Qu et al, 2013;Corretto et al, 2015;Avramov et al, 2016;Learman et al, 2019;Lu et al, 2019;Ortet et al, 2019;Corretto et al, 2020;Heidari et al, 2020;Martínez-Rodríguez et al, 2020;Mishra et al, 2021;Mitra et al, 2021) or promoting plant growth (Vílchez et al, 2018;Singh and Singh, 2019;García-Fontana et al, 2020;Yang et al, 2021). Moreover, many Microbacterium spp.…”

Section: Introductionmentioning

confidence: 99%

Draft genome sequence of Microbacterium fakhimisp. nov., a novel bacterium associated with the algaChlamydomonas reinhardtii

Fakhimi

Torres²,

Delgado-Luque³

et al. 2023

Preprint

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Microbacterium fakhimi sp. nov. has been isolated from a contaminated algal culture (Chlamydomonas reinhardtii). Its genome has been fully sequenced (3,753,259 base pairs) and a tentative annotation is provided (3,704 genes). Both, genome information and growth tests suggest that M. fakhimi sp. nov. is auxotroph for biotin and thiamine and unable to use sulfate as sulfur (S) source. S-reduced forms, such as methionine and cysteine can support M. fakhimi sp. nov. growth. The potential biotechnological interest of this bacteria is discussed here and in a related research paper (Fakhimi et al., 2023b).

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Complete Genome Sequences of Four Microbacterium Strains Isolated from Metal- and Radionuclide-Rich Soils

Abstract: Here, we present the genome sequences of four Microbacterium strains, which were isolated at different locations in Europe from metal- or radionuclide-rich soils. High-quality complete genome sequences were obtained with PacBio and Illumina data sets with an original two-step procedure.

Cited by 5 publications

References 17 publications

Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – a heavy metal hypertolerant and plant growth promoting bacterium

Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – a heavy metal hypertolerant and plant growth promoting bacterium

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Draft genome sequence of Microbacterium fakhimisp. nov., a novel bacterium associated with the algaChlamydomonas reinhardtii

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