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Genome Announc. 2017 September; 5(38): e01008-17.
Published online 2017 September 21. doi:  10.1128/genomeA.01008-17
PMCID: PMC5609425

Complete Genome Sequence of a Novel Bioflocculant-Producing Strain, Microbacterium paludicola CC3

ABSTRACT

Microbacterium paludicola CC3 exhibits the capability to produce polysaccharide bioflocculants. Here, we report the whole-genome sequence of M. paludicola CC3, which may be helpful in understanding the genetic basis of the biosynthesis of polysaccharide bioflocculants as well as in promoting its production and application in industrial fields.

GENOME ANNOUNCEMENT

Bioflocculants are mainly extracellular polymeric substances secreted by microorganisms (1) and are widely applied in microalgae harvest (2) and wastewater treatment (3), due to their harmless and biodegrading properties (4). The genome of several strains that can produce bioflocculants have been sequenced, including those of Paenibacillus shenyangensis, Agrobacterium tumefaciens F2, and Paenibacillus wulumuqiensis (5,7). However, the genomic data of bioflocculant-producing strains are still rare, which limits the identification of key enzymes and metabolic pathways that are involved in the biosynthesis of bioflocculants.

In this study, a novel bioflocculant-producing strain, Microbacterium paludicola CC3, was sequenced with the Pacific Biosciences (PacBio) RSII platform using P6-C4 chemistry. The resulting sequencing reads with 320.4-fold coverage were then de novo assembled using Hierarchical Genome Assembly Process (HGAP) (8, 9). Gene prediction was performed against the assembled CC3 genome with GeneMarkS (10). Functional characterization of predicted genes was based on a BLASTP search against GenBank’s nonredundant (NR) protein database, the database of the Clusters of Orthologous Groups of proteins (COG) (http://www.ncbi.nlm.nih.gov/COG/), and the Gene Ontology (GO) Consortium (http://www.geneontology.org/). The metabolic pathways were predicted using the KEGG Automatic Annotation Server (KAAS) (http://www.genome.jp/tools/kaas/). rRNAs and tRNAs were identified using Barrnap 0.4.2 (http://www.vicbioinformatics.com/software.barrnap.shtml) and tRNAscan-SE version 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/), respectively. The clustered regularly interspaced short palindromic repeat (CRISPR) elements were detected using PILER-CR (11).

One gapless circular contig was assembled, which corresponded to the chromosome of M. paludicola CC3. No plasmid sequences were detected. The chromosome was composed of 3,410,829 bp, with an average G+C content of 70.10%, which comprised 3,390 predicted genes, of which 3,209 were protein coding genes (CDSs), 32 were tRNA genes, 146 were rRNA genes, and 3 were microRNA genes. Pseudogenes and prophage genes were not identified, whereas 14 CRISPR candidates were detected in the genome of strain CC3. A series of genes encoding polysaccharide biosynthesis/modification proteins, such as mannose-1-phosphate guanylyltransferase (12), glucose-1-phosphate thymidylyltransferase (13), dolichol-phosphate mannosyltransferase (14), dTDP-4-dehydrorhamnose reductase (15), and genes involved in polysaccharide ABC-type transporters were detected, which may function in the biosynthesis of polysaccharide bioflocculant and transportation across membranes and cell walls (16, 17). In previous studies, the biomass wastes were directly used as carbon source of lignocellulose-degrading strains to produce various value-added products at a low cost (2, 18). Therefore, we are interested in the genes encoding the lignocellulose-degrading enzymes. Genes encoding xylanase, cellulose, and amylase were identified, thereby suggesting that strain CC3 can directly convert biomass waste into polysaccharide bioflocculants.

Accession number(s).

The sequence data for the genome of M. paludicola CC3 have been deposited to GenBank under the accession number CP018134; the version described in this paper is the first version. Strain CC3 has been deposited at the China General Microbiological Culture Collection Center (CGMCC 1.15930).

ACKNOWLEDGMENTS

This study was supported by the National Natural Science Foundation of China (grant 31300054), funds from the Natural Science Foundation of Jiangsu Province of China (grant BK20171163), the Natural Science Foundation of Xuzhou City (grant KC15N0014), and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Footnotes

Citation Liu W, Liu C, Sun D. 2017. Complete genome sequence of a novel bioflocculant-producing strain, Microbacterium paludicola CC3. Genome Announc 5:e01008-17. https://doi.org/10.1128/genomeA.01008-17.

REFERENCES

1. Liu C, Wang K, Jiang JH, Liu WJ, Wang JY 2015. A novel bioflocculant produced by a salt-tolerant, alkaliphilic and biofilm-forming strain Bacillus agaradhaerens C9 and its application in harvesting Chlorella minutissima UTEX2341. Biochem Eng J 93:166–172. doi:.10.1016/j.bej.2014.10.006 [Cross Ref]
2. Liu W, Zhao C, Jiang J, Lu Q, Hao Y, Wang L, Liu C 2015. Bioflocculant production from untreated corn stover using Cellulosimicrobium cellulans L804 isolate and its application to harvesting microalgae. Biotechnol Biofuels 8:170. doi:.10.1186/s13068-015-0354-4 [PMC free article] [PubMed] [Cross Ref]
3. Deng SB, Bai RB, Hu XM, Luo Q 2003. Characteristics of a bioflocculant produced by Bacillus mucilaginosus and its use in starch wastewater treatment. Appl Microbiol Biotechnol 60:588–593. doi:.10.1007/s00253-002-1159-5 [PubMed] [Cross Ref]
4. Salehizadeh H, Shojaosadati SA 2001. Extracellular biopolymeric flocculants: recent trends and biotechnological importance. Biotechnol Adv 19:371–385. doi:.10.1016/S0734-9750(01)00071-4 [PubMed] [Cross Ref]
5. Li A, Geng J, Cui D, Shu C, Zhang S, Yang J, Xing J, Wang J, Ma F, Hu S 2011. Genome sequence of Agrobacterium tumefaciens strain F2, a bioflocculant-producing bacterium. J Bacteriol 193:5531–5531. doi:.10.1128/JB.05690-11 [PMC free article] [PubMed] [Cross Ref]
6. Fu L, Jiang B, Liu J, Xin Z, Qian L, Hu X 2015. Genome sequence analysis of a flocculant-producing bacterium, Paenibacillus shenyangensis. Biotechnol Lett 38:447–453. doi:.10.1007/s10529-015-1990-2 [PubMed] [Cross Ref]
7. Wu Q, Zhu L, Jiang L, Xu X, Xu Q, Zhang Z, Huang H 2015. Genome sequence of Paenibacillus wulumuqiensis sp. nov., a bioflocculant-producing species. Genome Announc 3(4):e00795-15. doi:.10.1128/genomeA.00795-15 [PMC free article] [PubMed] [Cross Ref]
8. Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33:623–630. doi:.10.1038/nbt.3238 [PubMed] [Cross Ref]
9. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi:.10.1038/nmeth.2474 [PubMed] [Cross Ref]
10. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi:.10.1186/1471-2105-11-119 [PMC free article] [PubMed] [Cross Ref]
11. Edgar RC. 2007. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8:18. doi:.10.1186/1471-2105-8-18 [PMC free article] [PubMed] [Cross Ref]
12. Arakawa Y, Wacharotayankun R, Nagatsuka T, Ito H, Kato N, Ohta M 1995. Genomic organization of the Klebsiella pneumoniae cps region responsible for serotype K2 capsular polysaccharide synthesis in the virulent strain Chedid. J Bacteriol 177:1788–1796. doi:.10.1128/jb.177.7.1788-1796.1995 [PMC free article] [PubMed] [Cross Ref]
13. Parajuli N, Lee DS, Lee HC, Liou K, Sohng JK 2004. Cloning, expression and characterization of glucose-1-phosphate thymidylyltransferase (strmlA) from Thermus caldophilus. Biotechnol Lett 26:437–442. doi:.10.1023/B:BILE.0000018264.35237.86 [PubMed] [Cross Ref]
14. Kido N, Kobayashi H 2000. A single amino acid substitution in a mannosyltransferase, WbdA, converts the Escherichia coli O9 polysaccharide into O9a: generation of a new O-serotype group. J Bacteriol 182:2567–2573. doi:.10.1128/JB.182.9.2567-2573.2000 [PMC free article] [PubMed] [Cross Ref]
15. Reeves PR, Hobbs M, Valvano MA, Skurnik M, Whitfield C, Coplin D, Kido N, Klena J, Maskell D, Raetz CR, Rick PD 1996. Bacterial polysaccharide synthesis and gene nomenclature. Trends Microbiol 4:495–503. doi:.10.1016/S0966-842X(97)82912-5 [PubMed] [Cross Ref]
16. Zhao JY, Geng S, Xu L, Hu B, Sun JQ, Nie Y, Tang YQ, Wu XL 2016. Complete genome sequence of Defluviimonas alba Cai42(T), a microbial exopolysaccharides producer. J Biotechnol 239:9–12. doi:.10.1016/j.jbiotec.2016.09.017 [PubMed] [Cross Ref]
17. Schmid J, Sieber V, Rehm B 2015. Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies. Front Microbiol 6:496. doi:.10.3389/fmicb.2015.00496 [PMC free article] [PubMed] [Cross Ref]
18. Liu C, Hao Y, Jiang J, Liu W 2017. Valorization of untreated rice bran towards bioflocculant using a lignocellulose-degrading strain and its use in microalgal biomass harvest. Biotechnol Biofuels 10:90. doi:.10.1186/s13068-017-0780-6 [PMC free article] [PubMed] [Cross Ref]

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