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. 2015 May 14;3(3):e00432-15. doi: 10.1128/genomeA.00432-15

Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments

Erika Corretto a, Livio Antonielli a, Angela Sessitsch a, Petra Kidd b, Nele Weyens c, Günter Brader a,✉
PMCID: PMC4432332  PMID: 25977426

Abstract

Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants) can play a role in mobilization processes and in the phytoextraction of HM. Here, we report the whole-genome sequences and annotation of 10 Microbacterium spp. isolated from both HM-contaminated and -noncontaminated compartments.

GENOME ANNOUNCEMENT

Microbacterium spp. have been isolated from diverse environments, including soil, plants, water, and humans (1–4). They belong to the class Actinobacteria, known for the production of a rich spectrum of secondary metabolites, including organic acids, antibiotics, siderophores, and other chelators (5). Interestingly, several Microbacterium spp. have shown to be resistant to different HM and to influence the mobility of HM in contaminated soils (6–8). The influence on HM mobilization might be due to the secretion of specific metabolites, making these bacteria suitable candidates for not only the understanding of metal mobilization processes but also the improvement of phytoextraction techniques limited mainly by the plant biomass production and the rate of metal uptake (9, 10). Bacteria isolated from HM-contaminated environments can overcome these limitations by promoting plant growth and increasing HM availability. Therefore, we decided to sequence a set of Microbacterium sp. genomes of organisms isolated from different HM-contaminated sites in Europe and strains obtained from the DSMZ collection (http://www.dsmz.de/catalogues/catalogue-microorganisms.html). Based on related publications (11–15), we conclude that the DSMZ strains do not derive from HM-polluted environments (Table 1).

TABLE 1 .

Summary of isolate origins and genomic features

Microbacterium sp.a Isolate Source Viral sequence % estimated with PhyloSift No. of rRNAs in Barrnap/total no.b No. of tRNAs No. of ORFsc G+C content (%) L50d N50d No. of contigs Total bp Coverage (×) Accession no.
From HM noncontaminated environment
    M. azadirachtae NR_116502 DSM 23848 Rhizoplane of neem (Azadirachta indica) seedlings 28e 3/12 49 3,751 70.45 12 97,758 86 4,037,586 49.69 ± 16.7 JYIT00000000
    M. foliorum NR_025368 DSM 12966 Phyllosphere of grasses 10 5/11 47 3,324 68.7 6 151,883 46 3,558,318 74.75 ± 24.7 JYIU00000000
    M. ginsengisoli NR_041516 DSM 18659 Soil of ginseng field 24e 3/3 45 2,963 70.22 8 145,068 80 3,047,504 71.53 ± 29.4 JYIY00000000
    M. ketosireducens NR_024638 DSM 12510 Soil 26 3/12 49 3,481 70.27 10 115,384 57 3,922,598 56.55 ± 21.1 JYIZ00000000
    M. trichothecenolyticum NR_044937 DSM 8608 Soil 23e 3/15 48 4,074 70.16 8 220,592 41 4,524,308 132.14 ± 42.4 JYJA00000000
From HM contaminated environment
    M. oxydans JX185498 BEL4b Rhizosphere of Brassica napus (Lommel Field, Belgium) 25 3/9 49 3,589 68.27 3 408,688 26 3,807,916 189.68 ± 47.9 JYIW00000000
    M. oxydans JX185498 BEL163 Roots of Salix viminalis (Lommel Field, Belgium) 28e 4/16 44 3,545 68.03 6 164,861 30 3,692,080 153.17 ± 50.4 JYIV00000000
    M. hydrocarbonoxydans HG941786 SA35 Rhizosphere of Alyssum serpyllifolium subsp. lusitanicum (Portugal, Samil, Trás-os-Montes) 17e 5/11 55 3,663 68.52 3 545,806 10 3,953,585 165.98 ± 38.9 JYJB00000000
    Microbacterium sp. AB042083 SA39 Rhizosphere of Alyssum serpyllifolium subsp. lusitanicum (Portugal, Samil, Trás-os-Montes) 40e 4/13 50 3,732 68.26 7 232,853 39 3,862,900 94.19 ± 27.4 JXRU00000000
    M. azadirachtae KF150486 ARN176 Soil (Arnoldstein, Austria) 37 3/9 40 3,910 70.14 7 258,062 40 4,243,255 126.11 ± 36.7 JYIX00000000
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a

The number after the organism name refers to the 16S rRNA gene NCBI accession number of the closest described relative.

b

Number of rRNAs predicted by Barrnap/number of rRNAs estimated based on the coverage of the contigs containing rRNA genes.

c

ORFs, open reading frames.

d

L50 and N50 were calculated using QUAST. N50 is the contig length such that using longer or equal length contigs produces half (50%) the bases of the assembly. L50 is the minimal number of contigs that cover ≥50% of the total length.

e

Presence of viral sequence confirmed by PHAST.

Genomic DNA was extracted with a phenol-chloroform extraction protocol (16). The Nextera XT kit (Illumina, San Diego, CA) was used for library preparation, and whole-genome sequencing was performed using Illumina MiSeq (MiSeq reagent kit version 3). Raw reads were screened for PhiX contamination using Bowtie2 (17). Adapter and quality trimming were performed in Trimmomatic-0.32 (18). Overlapping reads were subsequently merged using FLASH (19), and long single reads and paired-end reads were assembled with SPAdes 3.1.0 (20). The assembly quality was estimated in QUAST 2.3 (21), and quality control of the mapping data was performed in Qualimap 1.0 (22). PhyloSift version 1.0.1 (23) was used to verify the genome completeness, assessing a list of 40 highly conserved single-copy marker genes, all of which were identified in each assembly. The phylogenetic analysis of the genomes showed no contamination, but a substantial number of viral sequences were detected (10 to 40% of the genome content), which was also confirmed by PHAST (24) for most genomes (Table 1). Moreover, we detected viral sequences in already-published Microbacterium sp. genomes in similar percentages.

Genome annotation (summarized in Table 1) was performed in Prokka (25), incorporating Prodigal 2.60, Aragorn, and Barrnap for the prediction of open reading frames (ORFs), tRNAs, and rRNAs, respectively. rRNA detection was confirmed with RNAmmer 1.2 (26). Using antiSMASH 2.0 (27), we detected gene clusters involved in the production of terpenoids in all sequenced strains, except the colorless isolate ARN176. Clusters involved in the production of polyketides and nonribosomal peptides were found in all strains but in DSM 18659 and in DSM 18659 and BEL163, respectively. A deeper comparison of the Microbacterium genes involved in HM resistance and mobilization is currently being performed and will be published in a subsequent report.

Nucleotide sequence accession numbers.

The nucleotide sequences have been deposited at the DDBJ/EMBL/GenBank under the accession numbers provided in Table 1.

ACKNOWLEDGMENT

This work was supported by the Austrian Science Fund FWF, project P 24569-B25.

Footnotes

Citation Corretto E, Antonielli L, Sessitsch A, Kidd P, Weyens N, Brader G. 2015. Draft genome sequences of 10 Microbacterium spp., with emphasis on heavy metal-contaminated environments. Genome Announc 3(3):e00432-15. doi:10.1128/genomeA.00432-15.

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