- Email: [email protected]
Complete genome sequence of marine Bacillus sp. Y-01, isolated from the plastics contamination in the Yellow Sea
Marine Genomics xxx (xxxx) xxx–xxx
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Complete genome sequence of marine Bacillus sp. Y-01, isolated from the plastics contamination in the Yellow Sea Xixi Wanga,1, Changfeng Qua,b, ⁎ Jinlai Miaoa,b,c,
⁎,1
, Wenyu Wanga, Zhou Zhenga,b, Fangming Liua, Meiling Ana,c,
a
Key Laboratory of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China c Medical College, Qingdao University, Qingdao 266071, China b
A R T I C LE I N FO
A B S T R A C T S
Keywords: Complete genome Bacillus Marine plastics contamination Microplastics Polypropylene
Plastics contamination in the environment has been an increasing ecological problem. Here we present the complete genome sequence of Bacillus sp. Y-01, isolated from plastic contamination samples in the Yellow Sea, which can utilize the polypropylene as the sole carbon and energy source. The strain has one circular chromosome of 5,130,901 bp in 8 contigs with a 38.24% GC content, consisting of 4996 protein-coding genes, 118 tRNA genes, as well as 40 rRNA operons as 5S-16S-23S rRNA. The complete genome sequence of Bacillus sp. Y-01 will provide useful genetic information to further detect the molecular mechanisms behind marine microplastics degradation.
1. Introduction Plastic wastes are contaminating the world ocean, and have adverse effects to marine ecosystems (Browne et al., 2008; Cole et al., 2013; GESAMP, 2015; Paço et al., 2017). Approximate 4.8–12.7 million tons plastics are released into the ocean every year (Jambeck et al., 2015). Microplastics, defined as plastic fragments below 5 mm in size (Thompson et al., 2004; Wright et al., 2013), play a key role in the ocean environment, which are formed by utilized products (primary microplastics) or fragementation of larger plastic item through physical abrasive and mainly UVB-photo oxidative degradation (secondary microplastics) (Auta et al., 2017). Many studies have shown that microplastics are now distributed in all oceans, even in remote locations (i.e. Antarctica and Arctic) (Obbard et al., 2014; Cincinelli et al., 2017) and at all depths (i.e. shoreline, surface water, and sediment) (Browne et al., 2011; Woodall et al., 2014; Qiu et al., 2015). Microplastics can cause physical harm and lead to bioaccumulation and bioamplification throughout the globe. Hence, microplastics pollution problems are becoming a major concern in oceans. However, very few studies have reported the biological degradation of microplastics or the use of microplastics to support microbial growth. The absence or low activity of catabolic enzymes that can break down the plastic constituents resulted in resistance to microbial degradation. In this study, we isolated a bacterial strain that grew on polypropylene
⁎
1
(PP) as sole carbon source from the marine plastics contamination in the Yellow Sea. The strain represented the genus Bacillus belonging to the family Bacillaceae with the class Bacilli, which is ubiquitous in the marine environment. 2. Data description The bacterium strain isolated from the plastic contamination samples in the Yellow Sea (36°40′17.12″ N, 121°30′19.47″ E). A portion of the contamination samples were transferred to the agar plates made from a sterilized artificial seawater medium containing polypropylene as the sole carbon source form. If the growth of bacterium occurred, the single colony from the plate was inoculated into a medium containing 2216E (peptone, 5 g; yeast extract, 1 g; natural seawater 1 l) and shaken at 140 rpm min−1 at 30 ± 1 °C (Fig. S1). The results of 16S rRNA gene sequence showed that the strain Y-01 could be assigned to the genus Bacillus sp. belonging to the family Bacillaceae within the phylum Firmicutes. The general features of Bacillus sp. Y-01 are summarized in Table 1 following the information of the MIGS checklist and environmental packages. The bacterium strain grew slowly at low temperature 15 °C (Fig. S2a). The most appropriate temperature was 30–40 °C. The strain stopped growing when the pH was 4 and 9 and the most appropriate pH was 7 (Fig. S2b). The treatments under high salinity treatment (80‰ and 96‰) postponed the bacterial growth (Fig. S2c).
Corresponding authors at: No. 6 of Xianxialing Road, Qingdao, China. E-mail addresses: cfqu@fio.org.cn (C. Qu), miaojinlai@fio.org.cn (J. Miao). These authors contributed equally to this work.
https://doi.org/10.1016/j.margen.2018.05.002 Received 12 April 2018; Received in revised form 7 May 2018; Accepted 7 May 2018 1874-7787/ © 2018 Elsevier B.V. All rights reserved.
Please cite this article as: Wang, X., Marine Genomics (2018), https://doi.org/10.1016/j.margen.2018.05.002
Marine Genomics xxx (xxxx) xxx–xxx
X. Wang et al.
Table 1 Classification, general features and genome sequencing information of Bacillus sp. Y-01 according to the MIGS 4.0 recommendations. Item
Description
Classification
Domain Bacteria Phylum Firmicutes Class Bacilli Family Bacillaceae Genus Bacillus Species Bacillus sp. Strain Y-01
General features Shape Gram-staining Motility Optimal temperature Optimal salinity Optimal pH MIGS 4.0 data Submitted to insdc Investigation type Project name Geographic location Latitude and longitude Collection date Environment (biome) Environment (feature) Environment (material) Number of replicons Reference for biomaterial Pathogenicity Observed biotic relationship Trophic level Relationship to oxygen Isolation and growth condition Sequencing method Assembly Finishing strategy
Table 2 Summary of general genomic features of Bacillus sp. Y-01. Bacillus sp. Y-01 Genome size (Mb) Chromosome size (Mb) Chromosome GC content (%) Chromosome CDS count Contigs GIs number 5S + 16S + 23S rRNA count tRNA count Plasmid count
Rod Positive Motile 30–40 °C 16–48‰ 6–8
5,892,113 5,130,901 38.24 4996 8 10 14 + 13 + 13 118 7
Orthologous Groups) (Tatusov et al., 2003), NR (Non-Redundant Protein Database databases) (Li et al., 2002), TCDB (Transporter Classification Database (Saier et al., 2014), Swiss-Prot and TrEMBL (Magrane and Consortium, 2011). The general genome features of strain Bacillus sp. Y-01 are summarized in Table 2. The sequencing generated 106,662 reads with mean read length 13,438 bp, totaling 1,433,409,375 bp. The size of the assembled completed genome is 5,130,901 bp with 38.24% GC content. Besides, it owns 7 plasmids, which GC content was 32.44%, 33.51%, 33.99%, 34.18%, 34.15%, 36.37%, and 34.12%, respectively. A total of 4996 predicted protein-coding sequences (CDSs) were obtained, with a gene length of 4,837,389 bp, accounting for 82.10% of the whole genome. Among the CDSs with known functions, 118 tRNA and 40 rRNA (operons made up of 5S, 16S and 23S) were detected. Meanwhile, 10 gene islands were identified by the method of IslandPath-DIOMB, with average lengths of 27,153 bp. The 3929 of CDSs were assigned a putative function in one of the COG categories. According to the gene annotation and the KEGG pathway analysis, Bacillus sp. Y-01 encoded a normal complement of genes for metabolic enzymes involved in glycan, amino acids and lipid biosynthesis, carbohydrates utilization and xenobiotics biodegradation, as well as essential genes for nucleotide metabolism, transcription and replication. It can been seen that the addition of microplastics (polypropylene less than 5 mm) increased the growth of Bacillus sp. Y-01 strain (Fig. 1), indicating that this bacterium Bacillus sp. Y-01 could utilize the polypropylene. The genome of Bacillus sp. Y-01 will provide a basis for studying the mechanisms of microplastics-degrading, especially the polypropylene-degrading, and contribute to the increasing scope and depth of marine Bacillus genome database, which will be our next prospects.
GenBank (CP024794) Bacteria Genome sequencing of Bacillus sp. Y-01 China: The Yellow Sea 36°40′17.12″ N, 121°30′19.47″ E 2016-06 Marine Marine plastics contamination Plastics contamination NA NA None Free living Heterotrophic Aerobic NA PacBio RS II SMRT Analysis v2.3 High quality draft 276.0 ×
The growth decreased gradually from 16‰ to 96‰. The optimal growth salinity of Bacillus sp. Y-01 was 16‰. In summary, the strain Bacillus sp. Y-01 is a mesophilic, euryhaline, aerobic, and heterotrophic bacterium. The genomic DNA of the strain Y-01 was extracted with the SDS method. Quality and quantity of harvested DNA was assessed using agarose gel electrophoresis, spectrophotometer (Nanodrop, GE Healthcare) and Qubit™ 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). The genome of Bacillus sp. Y-01 was sequenced by Single Molecule, Real-Time (SMRT) technology. Sequencing was performed at the Beijing Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). Briefly, the prepared DNA samples were sheared to 10 Kb by Covaris g-TUBE (Covaris, Woburn, MA, USA) and purified using an AMPure PB magnetic beads (Beckman-coulter, Fullerton, CA, UAS). A PacBio SMRT Bell Template Pre KIT (Pacific Biosciences, Mcnlo Park, CA, USA) was used to construct the library. Sequences were generated with a PacBio RS II instrument (Pacific Biosceiences, Menlo Park, CA, USA). The low quality reads were filtered by SMART portal (Version 3.2.0) software and the filtered reads were assembled by SOAPdenovo (http://soap.genomics.org.cn/soapdenovo.html) to generate one contig without gaps. GeneMarkS (Verison 4.17) program was used to retrieve the related coding gene (Besemer et al., 2001). Transfer RNAs (tRNA), ribosome RNAs (rRNA) and small RNA (sRNA) were predicted by tRNAscan-SE (Lowe and Eddy, 1997), rRNAmmer (Lagesen et al., 2007) BLAST against the Rfam database (Gardner et al., 2009), respectively. Gene islands were predicted with IslandViewer (Bertelli et al., 2017). Gene prediction was assembled by GeneMarks (Besemer et al., 2001). Annotation of the genomic sequence was carried out by BLAST against GO (Gene Ontology) (Ashburner et al., 2000), KEGG (Kyoto Encyclopedia of Genes and Genomes) (Kanehisa et al., 2006), COG (Clusters of
Fig. 1. Growth of Bacillus sp. Y-01 in the addition of 1 ml, 2 ml, 5 ml and 10 ml bacterial liquid with and without microplastics (Polypropylene: PP). 2
Marine Genomics xxx (xxxx) xxx–xxx
X. Wang et al.
3. Nucleotide sequence accession number
Browne, M.A., Dissanayake, A., Galloway, T.S., et al., 2008. Ingested microscopic plastic translocates to the circulatory system of the mussel, Mytilus edulis (L). Environ. Sci. Technol. 42 (13), 5026–5031. Browne, M.A., Crump, P., Niven, S.J., et al., 2011. Accumulation of microplastic on shorelines woldwide: sources and sinks. Environ. Sci. Technol. 45 (21), 9175–9179. Cincinelli, A., Scopetani, C., Chelazzi, D., et al., 2017. Microplastic in the surface waters of the Ross Sea (Antarctica): occurrence, distribution and characterization by FTIR. Chemosphere 175, 391–400. Cole, M., Lindeque, P., Fileman, E., et al., 2013. Microplastic ingestion by zooplankton. Environ. Sci. Technol. 47 (12), 6646–6655. Gardner, P.P., Daub, J., Tate, J.G., et al., 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37 (Database issue), D136. GESAMP, 2015. Sources, fate and effects of microplastics in the marine environment: a global assessment. In: Kershaw, P.J. (Ed.), Joint Group of Experts on the Scientific Aspects of Marine Environmental Protection Reports and Studies, pp. 90–96. Jambeck, J.R., Geyer, R., Wilcox, C., et al., 2015. Plastic waste inputs from land into the ocean. Science 347 (6223), 768–771. Kanehisa, M., Goto, S., Hattori, M., et al., 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34 (Database issue), 354–357. Lagesen, K., Hallin, P., Rødland, E.A., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35 (9), 3100. Li, W., Jaroszewski, L., Godzik, A., 2002. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18 (1), 77. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (5), 955. Magrane M and Consortium UP, 2011. UniProt Knowledgebase: a hub of integrated data. Database J. Biol. Database. Curat. 2011 (bar009), bar009. Obbard, R.W., Sadri, S., Wong, Y.Q., et al., 2014. Global warming releases microplastic legacy frozen in Arctic Sea ice. Earths Future 2 (6), 315–320. Paço, A., Duarte, K., Da, C.J., et al., 2017. Biodegradation of polyethylene microplastics by the marine fungus Zalerion maritimum. Sci. Total Environ. 586, 10–15. Qiu, Q., Peng, J., Yu, X., et al., 2015. Occurrence of microplastics in the coastal marine environment: first observation on sediment of China. Mar. Pollut. Bull. 98 (1–2), 274–280. Saier, M.H.J., Reddy, V.S., Tamang, D.G., et al., 2014. The transporter classification database. Nucleic Acids Res. 42 (Database issue), 251–258. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., et al., 2003. The COG database: an updated version includes eukaryotes. BMC Bioinform. 4 (1), 41. Thompson, R.C., Olsen, Y., Mitchell, R.P., et al., 2004. Lost at sea: where is all the plastic? Science 304 (5672), 838. Woodall, L.C., Sanchezvidal, A., Canals, M., et al., 2014. The deep sea is a major sink for microplastic debris. R. Soc. Open Sci. 1 (4), 140317. Wright, S.L., Thompson, R.C., Galloway, T.S., 2013. The physical impacts of microplastics on marine organisms: a review. Environ. Pollut. 178 (1), 483–492.
The genome sequence of Bacillus sp. Y-01 has been deposited at GenBank under the accession no. CP024794. The strain is available from the Key laboratory of marine bioactive substances, First Institute of Oceanology, State Oceanic Administration, China. Acknowledgements This work was funded by Key Research and Development Program of Shandong Province (No. 2018GHY115034), Natural Science Foundation of China (No. 41576187, No. 41776203), Basic Scientific Fund for National Public Research Institutes of China (No. 2016Q10), Key Research and Development Program of Shandong Province (No. 2016YYSP017, No. 2016ZDJS06A03, No. 2017GHY15112), Natural Science Foundation of China-Shandong Joint Fund (No. U1606403), Qingdao Entrepreneurship & Innovation Pioneers Program (No. 15-103-15-(44)-zch) and Innovative Development and Demonstration Project of Marine Economy (No. NBHY-2017-P2). Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.margen.2018.05.002. References Ashburner, M., Ball, C.A., Blake, J.A., et al., 2000. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25 (1), 25–29. Auta, H.S., Emenike, C.U., Fauziah, S.H., 2017. Distribution and importance of microplastics in the marine environment: a review of the sources, fate, effects, and potential solutions. Environ. Int. 102, 165. Bertelli, C., Laird, M.R., Williams, K.P., et al., 2017. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 45, W30–W35. Besemer, J., Lomsadze, A., Borodovsky, M., 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29 (12), 2607–2618.
3
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Complete genome sequence of marine Bacillus sp. Y-01, isolated from the plastics contamination in the Yellow Sea Xixi Wanga,1, Changfeng Qua,b, ⁎ Jinlai Miaoa,b,c,
⁎,1
, Wenyu Wanga, Zhou Zhenga,b, Fangming Liua, Meiling Ana,c,
a
Key Laboratory of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China c Medical College, Qingdao University, Qingdao 266071, China b
A R T I C LE I N FO
A B S T R A C T S
Keywords: Complete genome Bacillus Marine plastics contamination Microplastics Polypropylene
Plastics contamination in the environment has been an increasing ecological problem. Here we present the complete genome sequence of Bacillus sp. Y-01, isolated from plastic contamination samples in the Yellow Sea, which can utilize the polypropylene as the sole carbon and energy source. The strain has one circular chromosome of 5,130,901 bp in 8 contigs with a 38.24% GC content, consisting of 4996 protein-coding genes, 118 tRNA genes, as well as 40 rRNA operons as 5S-16S-23S rRNA. The complete genome sequence of Bacillus sp. Y-01 will provide useful genetic information to further detect the molecular mechanisms behind marine microplastics degradation.
1. Introduction Plastic wastes are contaminating the world ocean, and have adverse effects to marine ecosystems (Browne et al., 2008; Cole et al., 2013; GESAMP, 2015; Paço et al., 2017). Approximate 4.8–12.7 million tons plastics are released into the ocean every year (Jambeck et al., 2015). Microplastics, defined as plastic fragments below 5 mm in size (Thompson et al., 2004; Wright et al., 2013), play a key role in the ocean environment, which are formed by utilized products (primary microplastics) or fragementation of larger plastic item through physical abrasive and mainly UVB-photo oxidative degradation (secondary microplastics) (Auta et al., 2017). Many studies have shown that microplastics are now distributed in all oceans, even in remote locations (i.e. Antarctica and Arctic) (Obbard et al., 2014; Cincinelli et al., 2017) and at all depths (i.e. shoreline, surface water, and sediment) (Browne et al., 2011; Woodall et al., 2014; Qiu et al., 2015). Microplastics can cause physical harm and lead to bioaccumulation and bioamplification throughout the globe. Hence, microplastics pollution problems are becoming a major concern in oceans. However, very few studies have reported the biological degradation of microplastics or the use of microplastics to support microbial growth. The absence or low activity of catabolic enzymes that can break down the plastic constituents resulted in resistance to microbial degradation. In this study, we isolated a bacterial strain that grew on polypropylene
⁎
1
(PP) as sole carbon source from the marine plastics contamination in the Yellow Sea. The strain represented the genus Bacillus belonging to the family Bacillaceae with the class Bacilli, which is ubiquitous in the marine environment. 2. Data description The bacterium strain isolated from the plastic contamination samples in the Yellow Sea (36°40′17.12″ N, 121°30′19.47″ E). A portion of the contamination samples were transferred to the agar plates made from a sterilized artificial seawater medium containing polypropylene as the sole carbon source form. If the growth of bacterium occurred, the single colony from the plate was inoculated into a medium containing 2216E (peptone, 5 g; yeast extract, 1 g; natural seawater 1 l) and shaken at 140 rpm min−1 at 30 ± 1 °C (Fig. S1). The results of 16S rRNA gene sequence showed that the strain Y-01 could be assigned to the genus Bacillus sp. belonging to the family Bacillaceae within the phylum Firmicutes. The general features of Bacillus sp. Y-01 are summarized in Table 1 following the information of the MIGS checklist and environmental packages. The bacterium strain grew slowly at low temperature 15 °C (Fig. S2a). The most appropriate temperature was 30–40 °C. The strain stopped growing when the pH was 4 and 9 and the most appropriate pH was 7 (Fig. S2b). The treatments under high salinity treatment (80‰ and 96‰) postponed the bacterial growth (Fig. S2c).
Corresponding authors at: No. 6 of Xianxialing Road, Qingdao, China. E-mail addresses: cfqu@fio.org.cn (C. Qu), miaojinlai@fio.org.cn (J. Miao). These authors contributed equally to this work.
https://doi.org/10.1016/j.margen.2018.05.002 Received 12 April 2018; Received in revised form 7 May 2018; Accepted 7 May 2018 1874-7787/ © 2018 Elsevier B.V. All rights reserved.
Please cite this article as: Wang, X., Marine Genomics (2018), https://doi.org/10.1016/j.margen.2018.05.002
Marine Genomics xxx (xxxx) xxx–xxx
X. Wang et al.
Table 1 Classification, general features and genome sequencing information of Bacillus sp. Y-01 according to the MIGS 4.0 recommendations. Item
Description
Classification
Domain Bacteria Phylum Firmicutes Class Bacilli Family Bacillaceae Genus Bacillus Species Bacillus sp. Strain Y-01
General features Shape Gram-staining Motility Optimal temperature Optimal salinity Optimal pH MIGS 4.0 data Submitted to insdc Investigation type Project name Geographic location Latitude and longitude Collection date Environment (biome) Environment (feature) Environment (material) Number of replicons Reference for biomaterial Pathogenicity Observed biotic relationship Trophic level Relationship to oxygen Isolation and growth condition Sequencing method Assembly Finishing strategy
Table 2 Summary of general genomic features of Bacillus sp. Y-01. Bacillus sp. Y-01 Genome size (Mb) Chromosome size (Mb) Chromosome GC content (%) Chromosome CDS count Contigs GIs number 5S + 16S + 23S rRNA count tRNA count Plasmid count
Rod Positive Motile 30–40 °C 16–48‰ 6–8
5,892,113 5,130,901 38.24 4996 8 10 14 + 13 + 13 118 7
Orthologous Groups) (Tatusov et al., 2003), NR (Non-Redundant Protein Database databases) (Li et al., 2002), TCDB (Transporter Classification Database (Saier et al., 2014), Swiss-Prot and TrEMBL (Magrane and Consortium, 2011). The general genome features of strain Bacillus sp. Y-01 are summarized in Table 2. The sequencing generated 106,662 reads with mean read length 13,438 bp, totaling 1,433,409,375 bp. The size of the assembled completed genome is 5,130,901 bp with 38.24% GC content. Besides, it owns 7 plasmids, which GC content was 32.44%, 33.51%, 33.99%, 34.18%, 34.15%, 36.37%, and 34.12%, respectively. A total of 4996 predicted protein-coding sequences (CDSs) were obtained, with a gene length of 4,837,389 bp, accounting for 82.10% of the whole genome. Among the CDSs with known functions, 118 tRNA and 40 rRNA (operons made up of 5S, 16S and 23S) were detected. Meanwhile, 10 gene islands were identified by the method of IslandPath-DIOMB, with average lengths of 27,153 bp. The 3929 of CDSs were assigned a putative function in one of the COG categories. According to the gene annotation and the KEGG pathway analysis, Bacillus sp. Y-01 encoded a normal complement of genes for metabolic enzymes involved in glycan, amino acids and lipid biosynthesis, carbohydrates utilization and xenobiotics biodegradation, as well as essential genes for nucleotide metabolism, transcription and replication. It can been seen that the addition of microplastics (polypropylene less than 5 mm) increased the growth of Bacillus sp. Y-01 strain (Fig. 1), indicating that this bacterium Bacillus sp. Y-01 could utilize the polypropylene. The genome of Bacillus sp. Y-01 will provide a basis for studying the mechanisms of microplastics-degrading, especially the polypropylene-degrading, and contribute to the increasing scope and depth of marine Bacillus genome database, which will be our next prospects.
GenBank (CP024794) Bacteria Genome sequencing of Bacillus sp. Y-01 China: The Yellow Sea 36°40′17.12″ N, 121°30′19.47″ E 2016-06 Marine Marine plastics contamination Plastics contamination NA NA None Free living Heterotrophic Aerobic NA PacBio RS II SMRT Analysis v2.3 High quality draft 276.0 ×
The growth decreased gradually from 16‰ to 96‰. The optimal growth salinity of Bacillus sp. Y-01 was 16‰. In summary, the strain Bacillus sp. Y-01 is a mesophilic, euryhaline, aerobic, and heterotrophic bacterium. The genomic DNA of the strain Y-01 was extracted with the SDS method. Quality and quantity of harvested DNA was assessed using agarose gel electrophoresis, spectrophotometer (Nanodrop, GE Healthcare) and Qubit™ 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). The genome of Bacillus sp. Y-01 was sequenced by Single Molecule, Real-Time (SMRT) technology. Sequencing was performed at the Beijing Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). Briefly, the prepared DNA samples were sheared to 10 Kb by Covaris g-TUBE (Covaris, Woburn, MA, USA) and purified using an AMPure PB magnetic beads (Beckman-coulter, Fullerton, CA, UAS). A PacBio SMRT Bell Template Pre KIT (Pacific Biosciences, Mcnlo Park, CA, USA) was used to construct the library. Sequences were generated with a PacBio RS II instrument (Pacific Biosceiences, Menlo Park, CA, USA). The low quality reads were filtered by SMART portal (Version 3.2.0) software and the filtered reads were assembled by SOAPdenovo (http://soap.genomics.org.cn/soapdenovo.html) to generate one contig without gaps. GeneMarkS (Verison 4.17) program was used to retrieve the related coding gene (Besemer et al., 2001). Transfer RNAs (tRNA), ribosome RNAs (rRNA) and small RNA (sRNA) were predicted by tRNAscan-SE (Lowe and Eddy, 1997), rRNAmmer (Lagesen et al., 2007) BLAST against the Rfam database (Gardner et al., 2009), respectively. Gene islands were predicted with IslandViewer (Bertelli et al., 2017). Gene prediction was assembled by GeneMarks (Besemer et al., 2001). Annotation of the genomic sequence was carried out by BLAST against GO (Gene Ontology) (Ashburner et al., 2000), KEGG (Kyoto Encyclopedia of Genes and Genomes) (Kanehisa et al., 2006), COG (Clusters of
Fig. 1. Growth of Bacillus sp. Y-01 in the addition of 1 ml, 2 ml, 5 ml and 10 ml bacterial liquid with and without microplastics (Polypropylene: PP). 2
Marine Genomics xxx (xxxx) xxx–xxx
X. Wang et al.
3. Nucleotide sequence accession number
Browne, M.A., Dissanayake, A., Galloway, T.S., et al., 2008. Ingested microscopic plastic translocates to the circulatory system of the mussel, Mytilus edulis (L). Environ. Sci. Technol. 42 (13), 5026–5031. Browne, M.A., Crump, P., Niven, S.J., et al., 2011. Accumulation of microplastic on shorelines woldwide: sources and sinks. Environ. Sci. Technol. 45 (21), 9175–9179. Cincinelli, A., Scopetani, C., Chelazzi, D., et al., 2017. Microplastic in the surface waters of the Ross Sea (Antarctica): occurrence, distribution and characterization by FTIR. Chemosphere 175, 391–400. Cole, M., Lindeque, P., Fileman, E., et al., 2013. Microplastic ingestion by zooplankton. Environ. Sci. Technol. 47 (12), 6646–6655. Gardner, P.P., Daub, J., Tate, J.G., et al., 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37 (Database issue), D136. GESAMP, 2015. Sources, fate and effects of microplastics in the marine environment: a global assessment. In: Kershaw, P.J. (Ed.), Joint Group of Experts on the Scientific Aspects of Marine Environmental Protection Reports and Studies, pp. 90–96. Jambeck, J.R., Geyer, R., Wilcox, C., et al., 2015. Plastic waste inputs from land into the ocean. Science 347 (6223), 768–771. Kanehisa, M., Goto, S., Hattori, M., et al., 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34 (Database issue), 354–357. Lagesen, K., Hallin, P., Rødland, E.A., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35 (9), 3100. Li, W., Jaroszewski, L., Godzik, A., 2002. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18 (1), 77. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (5), 955. Magrane M and Consortium UP, 2011. UniProt Knowledgebase: a hub of integrated data. Database J. Biol. Database. Curat. 2011 (bar009), bar009. Obbard, R.W., Sadri, S., Wong, Y.Q., et al., 2014. Global warming releases microplastic legacy frozen in Arctic Sea ice. Earths Future 2 (6), 315–320. Paço, A., Duarte, K., Da, C.J., et al., 2017. Biodegradation of polyethylene microplastics by the marine fungus Zalerion maritimum. Sci. Total Environ. 586, 10–15. Qiu, Q., Peng, J., Yu, X., et al., 2015. Occurrence of microplastics in the coastal marine environment: first observation on sediment of China. Mar. Pollut. Bull. 98 (1–2), 274–280. Saier, M.H.J., Reddy, V.S., Tamang, D.G., et al., 2014. The transporter classification database. Nucleic Acids Res. 42 (Database issue), 251–258. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., et al., 2003. The COG database: an updated version includes eukaryotes. BMC Bioinform. 4 (1), 41. Thompson, R.C., Olsen, Y., Mitchell, R.P., et al., 2004. Lost at sea: where is all the plastic? Science 304 (5672), 838. Woodall, L.C., Sanchezvidal, A., Canals, M., et al., 2014. The deep sea is a major sink for microplastic debris. R. Soc. Open Sci. 1 (4), 140317. Wright, S.L., Thompson, R.C., Galloway, T.S., 2013. The physical impacts of microplastics on marine organisms: a review. Environ. Pollut. 178 (1), 483–492.
The genome sequence of Bacillus sp. Y-01 has been deposited at GenBank under the accession no. CP024794. The strain is available from the Key laboratory of marine bioactive substances, First Institute of Oceanology, State Oceanic Administration, China. Acknowledgements This work was funded by Key Research and Development Program of Shandong Province (No. 2018GHY115034), Natural Science Foundation of China (No. 41576187, No. 41776203), Basic Scientific Fund for National Public Research Institutes of China (No. 2016Q10), Key Research and Development Program of Shandong Province (No. 2016YYSP017, No. 2016ZDJS06A03, No. 2017GHY15112), Natural Science Foundation of China-Shandong Joint Fund (No. U1606403), Qingdao Entrepreneurship & Innovation Pioneers Program (No. 15-103-15-(44)-zch) and Innovative Development and Demonstration Project of Marine Economy (No. NBHY-2017-P2). Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.margen.2018.05.002. References Ashburner, M., Ball, C.A., Blake, J.A., et al., 2000. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25 (1), 25–29. Auta, H.S., Emenike, C.U., Fauziah, S.H., 2017. Distribution and importance of microplastics in the marine environment: a review of the sources, fate, effects, and potential solutions. Environ. Int. 102, 165. Bertelli, C., Laird, M.R., Williams, K.P., et al., 2017. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 45, W30–W35. Besemer, J., Lomsadze, A., Borodovsky, M., 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29 (12), 2607–2618.
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