Draft genome sequence of Chryseobacterium limigenitum SUR2T (LMG 28734T) isolated from dehydrated sludge

Jure Škraban Nikos C. Kyrpides Nicole Shapiro William B. Whitman Janja Trček About the authors

ABSTRACT

The type strain SUR2 of the novel species Chryseobacterium limigenitum was isolated from a dehydrated sludge of the municipal sewage treatment plant in Dogoše near Maribor in Slovenia. The draft genome, with 60 contigs, 4,697,725 bp, 34.4% of G+C content, was obtained using the Illumina HiSeq 2500-1 platform. Joint Genome Institute Microbial Genome Annotation Pipeline (MGAP v.4) has identified 4322 protein-coding sequences including resistance genes against arsenic and other heavy metals. In addition, a subclass B3 metallo-β-lactamase, which confers resistance to penicillins, cephalosporins and carbapenems, was also present in the genome. The genome sequence provides important information regarding bioremediation potential and pathogenic properties of this newly identified species.

Keywords:
Chryseobacterium limigenitum; Genome; Arsenite; Lactamase

Since its first description two decades ago,11 Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. New perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Evol Microbiol. 1994;44:827-831. the genus Chryseobacterium now includes a large number of species often isolated from industrially degraded environments.22 Pires C, Carvalho MF, De Marco P, Magan N, Castro PML. Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. Int J Syst Evol Microbiol. 2010;60:402-407. Many members of the genus are capable of bioremediation of heavy metals and organochlorine pesticides,33 Qu J, Xua Y, Aia G-M, Liu Y, Liu ZP. Novel Chryseobacterium sp. PYR2 degrades various organochlorine pesticides (OCPs) and achieves enhancing removal and complete degradation of DDT in highly contaminated soil. J Environ Manage. 2015;161:350-357. and some species (Chryseobacterium indologenes) cause nosocomial infections.44 Zeba B, De Luca F, Dubus A, et al. IND-6, a highly divergent IND-type metallo-β-lactamase from Chryseobacterium indologenes strain 597 isolated in Burkina Faso. Antimicrob Agents Chemother. 2009;53:4320-4326. Here we report a draft genome sequence of a new species Chryseobacterium limigenitum (type strain SUR2), which was isolated from dehydrated sludge of the municipal sewage treatment plant in Dogoše near Maribor in Slovenia.55 Kämpfer P, Trček J, Skok B, Šorgo A, Glaeser SP. Chryseobacterium limigenitum sp. nov., isolated from dehydrated sludge. Antonie van Leeuwenhoek. 2015;107:1633-1638.

SUR2 was cultured on nutrient agar (NA, Sigma-Aldrich) for 48 h at 30 °C. Genomic DNA was extracted with NucleoSpin Tissue kit (Macherey-Nagel) using the manufacturers protocol. Sequencing was performed at the DOE Joint Genome Institute (JGI) using the Illumina HiSeq 2000-1TB platform, which generated 9,287,994 reads totaling 1393.2 Mbp. The reads were filtered using BBTools software package (http://sourceforge.net/projects/bbmap) and assembled with Velvet (version 1.2.07).66 Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821-829. Wgsim (version 0.3.0) (https://github.com/lh3/wgsim) was used to generate 1-3 kbp simulated paired end reads from Velvet contigs longer than 500 bp and finally assembled using Allpaths-LG (version r46652).77 Gnerre S, MacCallum I. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS. 2011;108:1513-1518. The final draft assembly contained 60 scaffolds (N50 = 193.444 kb), totaling 4,697,725 bp in size and a coverage of 292.7x. The G+C content was 34.4%. JGI Microbial Genome Annotation Pipeline (MGAP v.4)88 Huntemann M, Ivanova NN, Mavromatis K, et al. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci. 2015;10:86. was used for annotation of the genome's 4322 protein-coding sequences (CDSs), 58 tRNAs, 1 rRNA and 50 ncRNAs.

C. limigenitum SUR2 has two operons composed of a transcriptional regulator (ArsR), an unannotated protein of 155 aa, followed by an arsenate reductase (ArsC), and an arsenite efflux pump (ArsB). Arsenate reduction to the more soluble arsenite and its expulsion is a detoxification mechanism by which the strain mobilizes arsenic, which can be deleterious to water environments.99 Ahmann D, Krumholz LR, Hemond HF, Lovley DR, Morel FMM. Microbial mobilization of arsenic from sediments of the Aberjona watershed. Environ Sci Technol. 1997;31:2923-2930. However, reduction to arsenite, followed by precipitation by sulfide could be applied for cleaning contaminated areas in the future.1010 Chung J, Li X, Rittmann BE. Bio-reduction of arsenate using a hydrogen-based membrane biofilm reactor. Chemosphere. 2006;65:24-34. Additionally, other heavy metal resistance genes (cobalt-zinc-cadmium resistance protein CzcA) and the corresponding efflux pumps have been identified. These genes are evidence for an adaptation to an environment polluted with heavy metals.

Some members of the genus (C. indologenes) cause nosocomial infections due to their resistance against most β-lactams.44 Zeba B, De Luca F, Dubus A, et al. IND-6, a highly divergent IND-type metallo-β-lactamase from Chryseobacterium indologenes strain 597 isolated in Burkina Faso. Antimicrob Agents Chemother. 2009;53:4320-4326.C. limigenitum SUR2 contained a subclass B3 metallo-β-lactamase that shares 81% identity to a recently identified CPS-1 lactamase found in Chryseobacterium piscium (WP_063857696.1). CPS-1 efficiently hydrolyses penicillins, cephalosporins, and carbapenems.1111 Gudeta DD, Pollini S, Docquier J-D, Bortolaia B, Rossolini GM, Guardabassi L. Biochemical characterization of CPS-1, a subclass B3 metallo-β-lactamase from a Chryseobacterium piscium soil isolate. Antimicrob Agents Chemother. 2016;60:1869-1873. Additionally, MFS efflux pumps inferring resistance to tetracyclin and fosmidomycin, multidrug resistance transporters of EmrB/QacA subfamily, MATE and DHA2 families are also present. Further analysis of the draft genome will shed more light on the possible bioremediation potential and pathogenic properties of this newly identified species.

The genome sequence has been deposited in the European Nucleotide Archive (ENA) under the accession number FPKW01000000, the version described in this paper is the first version.

Acknowledgements

The genome sequencing described in this work was conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research has been partially funded by the Slovenian Research Agency through program P2-0006.

References

  • 1
    Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. New perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Evol Microbiol 1994;44:827-831.
  • 2
    Pires C, Carvalho MF, De Marco P, Magan N, Castro PML. Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. Int J Syst Evol Microbiol 2010;60:402-407.
  • 3
    Qu J, Xua Y, Aia G-M, Liu Y, Liu ZP. Novel Chryseobacterium sp. PYR2 degrades various organochlorine pesticides (OCPs) and achieves enhancing removal and complete degradation of DDT in highly contaminated soil. J Environ Manage 2015;161:350-357.
  • 4
    Zeba B, De Luca F, Dubus A, et al. IND-6, a highly divergent IND-type metallo-β-lactamase from Chryseobacterium indologenes strain 597 isolated in Burkina Faso. Antimicrob Agents Chemother 2009;53:4320-4326.
  • 5
    Kämpfer P, Trček J, Skok B, Šorgo A, Glaeser SP. Chryseobacterium limigenitum sp. nov., isolated from dehydrated sludge. Antonie van Leeuwenhoek 2015;107:1633-1638.
  • 6
    Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821-829.
  • 7
    Gnerre S, MacCallum I. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS 2011;108:1513-1518.
  • 8
    Huntemann M, Ivanova NN, Mavromatis K, et al. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 2015;10:86.
  • 9
    Ahmann D, Krumholz LR, Hemond HF, Lovley DR, Morel FMM. Microbial mobilization of arsenic from sediments of the Aberjona watershed. Environ Sci Technol 1997;31:2923-2930.
  • 10
    Chung J, Li X, Rittmann BE. Bio-reduction of arsenate using a hydrogen-based membrane biofilm reactor. Chemosphere 2006;65:24-34.
  • 11
    Gudeta DD, Pollini S, Docquier J-D, Bortolaia B, Rossolini GM, Guardabassi L. Biochemical characterization of CPS-1, a subclass B3 metallo-β-lactamase from a Chryseobacterium piscium soil isolate. Antimicrob Agents Chemother 2016;60:1869-1873.

Publication Dates

  • Publication in this collection
    Jan-Mar 2018

History

  • Received
    21 Dec 2016
  • Accepted
    1 Mar 2017
Sociedade Brasileira de Microbiologia USP - ICB III - Dep. de Microbiologia, Sociedade Brasileira de Microbiologia, Av. Prof. Lineu Prestes, 2415, Cidade Universitária, 05508-900 São Paulo, SP - Brasil, Ramal USP 7979, Tel. / Fax: (55 11) 3813-9647 ou 3037-7095 - São Paulo - SP - Brazil
E-mail: bjm@sbmicrobiologia.org.br