Adaptive Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River Sediment

Song, Da; Chen, Xingjuan; Xu, Meiying; Hai, Rong; Zhou, Aifen; Tian, Renmao; Van Nostrand, Joy D.; Kempher, Megan L.; Guo, Jun; Sun, Guoping; Zhou, Jizhong

doi:10.3389/fmicb.2019.02263

Title: Adaptive Evolution of Sphingobium hydrophobicum C1^T in Electronic Waste Contaminated River Sediment

Journal Article · 02 October 2019 · Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.02263 · OSTI ID:1580867

Song, Da ^[1]; Chen, Xingjuan ^[2]; Xu, Meiying ^[2]; Hai, Rong ^[3]; Zhou, Aifen ^[4]; Tian, Renmao ^[4]; Van Nostrand, Joy D. ^[4]; Kempher, Megan L. ^[4]; Guo, Jun ^[2]; Sun, Guoping ^[2]; Zhou, Jizhong ^[4]

South China Univ. of Technology (SCUT), Guangzhou (China); Guangdong Academy of Sciences, Guangzhou (China). State Key Lab. of Applied Microbiology Southern China, Guangdong Provincial Key Lab. of Microbial Culture Collection and Application, Guangdong Inst. of Microbiology
Guangdong Academy of Sciences, Guangzhou (China). State Key Lab. of Applied Microbiology Southern China, Guangdong Provincial Key Lab. of Microbial Culture Collection and Application, Guangdong Inst. of Microbiology
Univ. of California, Riverside, CA (United States)
Univ. of Oklahoma, Norman, OK (United States)

Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1^T, characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1^T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1^T and other Sphingobium strains, numerous C1^T-unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1^T. Moreover, presence of type IV secretion systems may allow strain C1^T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1580867

Journal Information:: Frontiers in Microbiology, Vol. 10; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 6 works

Citation information provided by
Web of Science

References (97)

Sphingobium fuliginis HC3: A Novel and Robust Isolated Biphenyl- and Polychlorinated Biphenyls-Degrading Bacterium without Dead-End Intermediates Accumulation Hu, Jinxing; Qian, Mingrong; Zhang, Qian PLOS ONE, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pone.0122740	journal	April 2015
Phthalate esters contamination in soil and plants on agricultural land near an electronic waste recycling site Ma, Ting Ting; Christie, Peter; Luo, Yong Ming Environmental Geochemistry and Health, Vol. 35, Issue 4 https://doi.org/10.1007/s10653-012-9508-5	journal	December 2012
Evolution Under Environmental Stress at Macro- and Microscales Nevo, Eviatar Genome Biology and Evolution, Vol. 3 https://doi.org/10.1093/gbe/evr052	journal	January 2011
New mechanisms of bacterial arsenic resistance Yang, Hung-Chi; Rosen, Barry P. Biomedical Journal, Vol. 39, Issue 1 https://doi.org/10.1016/j.bj.2015.08.003	journal	February 2016
Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins Rodgers, Kenton R.; Lukat-Rodgers, Gudrun S. Journal of Inorganic Biochemistry, Vol. 99, Issue 4 https://doi.org/10.1016/j.jinorgbio.2005.02.016	journal	April 2005
Microbial Bioleaching of Ag, Au and Cu from Printed Circuit Boards of Mobile Phones Díaz-Martínez, María E.; Argumedo-Delira, Rosalba; Sánchez-Viveros, Gabriela Current Microbiology, Vol. 76, Issue 5 https://doi.org/10.1007/s00284-019-01646-3	journal	February 2019
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Laslett, Dean; Canback, Bjorn Nucleic Acids Research, Vol. 32, Issue 1, p. 11-16 https://doi.org/10.1093/nar/gkh152	journal	January 2004
RNAmmer: consistent and rapid annotation of ribosomal RNA genes Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas Nucleic Acids Research, Vol. 35, Issue 9 https://doi.org/10.1093/nar/gkm160	journal	April 2007
Pseudomonas aeruginosa PAO1 exopolysaccharides are important for mixed species biofilm community development and stress tolerance Periasamy, Saravanan; Nair, Harikrishnan A. S.; Lee, Kai W. K. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00851	journal	August 2015
ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes Varani, Alessandro M.; Siguier, Patricia; Gourbeyre, Edith Genome Biology, Vol. 12, Issue 3 https://doi.org/10.1186/gb-2011-12-3-r30	journal	January 2011
Sphingobium hydrophobicum sp. nov., a hydrophobic bacterium isolated from electronic-waste-contaminated sediment Chen, Xingjuan; Wang, Haiji; Xu, Jingjing International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 10 https://doi.org/10.1099/ijsem.0.001287	journal	October 2016
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Darling, A. C. E. Genome Research, Vol. 14, Issue 7 https://doi.org/10.1101/gr.2289704	journal	June 2004
Experimental study of the pH, ionic strength, and reversibility behavior of bacteria–mineral adsorption Yee, Nathan; Fein, Jeremy B.; Daughney, Christopher J. Geochimica et Cosmochimica Acta, Vol. 64, Issue 4 https://doi.org/10.1016/S0016-7037(99)00342-7	journal	February 2000
Gene Amplification and Adaptive Evolution in Bacteria Andersson, Dan I.; Hughes, Diarmaid Annual Review of Genetics, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-genet-102108-134805	journal	December 2009
Autecological properties of soil sphingomonads involved in the degradation of polycyclic aromatic hydrocarbons Cunliffe, Michael; Kertesz, Michael A. Applied Microbiology and Biotechnology, Vol. 72, Issue 5 https://doi.org/10.1007/s00253-006-0374-x	journal	March 2006
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1 Wang, Juanping; Wang, Chang; Li, Jionghui Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02238	journal	September 2018
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons Alikhan, Nabil-Fareed; Petty, Nicola K.; Ben Zakour, Nouri L. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-402	journal	August 2011
Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation Gan, Han; Hudson, André O.; Rahman, Ahmad Yamin BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-431	journal	January 2013
ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments Zhang, Zhang; Xiao, Jingfa; Wu, Jiayan Biochemical and Biophysical Research Communications, Vol. 419, Issue 4 https://doi.org/10.1016/j.bbrc.2012.02.101	journal	March 2012
Aerobic degradation of BDE-209 by Enterococcus casseliflavus: Isolation, identification and cell changes during degradation process Tang, Shaoyu; Yin, Hua; Chen, Shuona Journal of Hazardous Materials, Vol. 308 https://doi.org/10.1016/j.jhazmat.2016.01.062	journal	May 2016
Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA García-Romero, Inmaculada; Pérez-Pulido, Antonio J.; González-Flores, Yolanda Elisabet BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2411-1	journal	February 2016
PHASTER: a better, faster version of the PHAST phage search tool Arndt, David; Grant, Jason R.; Marcu, Ana Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw387	journal	May 2016
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes Barakat, Mohamed; Ortet, Philippe; Whitworth, David E. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-269	journal	January 2013
Molecular characteristics of xenobiotic-degrading sphingomonads Stolz, Andreas Applied Microbiology and Biotechnology, Vol. 81, Issue 5 https://doi.org/10.1007/s00253-008-1752-3	journal	November 2008
Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya mBio, Vol. 7, Issue 2 https://doi.org/10.1128/mBio.02234-15	journal	April 2016
Microbial degradation of aromatic compounds — from one strategy to four Fuchs, Georg; Boll, Matthias; Heider, Johann Nature Reviews Microbiology, Vol. 9, Issue 11, p. 803-816 https://doi.org/10.1038/nrmicro2652	journal	October 2011
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity Wang, Y.; Tang, H.; DeBarry, J. D. Nucleic Acids Research, Vol. 40, Issue 7 https://doi.org/10.1093/nar/gkr1293	journal	January 2012
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets Bertelli, Claire; Laird, Matthew R.; Williams, Kelly P. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx343	journal	May 2017
Role and mechanism of cell-surface hydrophobicity in the adaptation of Sphingobium hydrophobicum to electronic-waste contaminated sediment Chen, Xingjuan; Song, Da; Xu, Jingjing Applied Microbiology and Biotechnology, Vol. 102, Issue 6 https://doi.org/10.1007/s00253-017-8734-2	journal	February 2018
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro Molecular Biology and Evolution, Vol. 34, Issue 8 https://doi.org/10.1093/molbev/msx148	journal	April 2017
Study of the Degradation Activity and the Strategies to Promote the Bioavailability of Phenanthrene by Sphingomonas paucimobilis Strain 20006FA Coppotelli, Bibiana M.; Ibarrolaza, Agustin; Dias, Romina L. Microbial Ecology, Vol. 59, Issue 2 https://doi.org/10.1007/s00248-009-9563-3	journal	July 2009
Decolorization of bromoamine acid by a newly isolated strain of Sphingomonas xenophaga QYY and its resting cells Qu, Yuanyuan; Wang, Jing; Zhou, Jiti Biochemical Engineering Journal, Vol. 27, Issue 2 https://doi.org/10.1016/j.bej.2005.08.005	journal	December 2005
Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide Tabata, Michiro; Ohhata, Satoshi; Nikawadori, Yuki DNA Research, Vol. 23, Issue 6 https://doi.org/10.1093/dnares/dsw041	journal	August 2016
Molecular characteristics of xenobiotic-degrading sphingomonads Stolz, Andreas Applied Microbiology and Biotechnology, Vol. 81, Issue 5 https://doi.org/10.1007/s00253-008-1752-3	journal	November 2008
Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways Verma, Helianthous; Kumar, Roshan; Oldach, Phoebe BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-1014	journal	January 2014
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons Alikhan, Nabil-Fareed; Petty, Nicola K.; Ben Zakour, Nouri L. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-402	journal	August 2011
Bacterial Exopolysaccharide mediated heavy metal removal: A Review on biosynthesis, mechanism and remediation strategies Gupta, Pratima; Diwan, Batul Biotechnology Reports, Vol. 13 https://doi.org/10.1016/j.btre.2016.12.006	journal	March 2017
Carotenoids Play a Positive Role in the Degradation of Heterocycles by Sphingobium yanoikuyae Liu, Xiaorui; Gai, Zhonghui; Tao, Fei PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0039522	journal	June 2012
Ecological Effects of Combined Pollution Associated with E-Waste Recycling on the Composition and Diversity of Soil Microbial Communities Liu, Jun; He, Xiao-xin; Lin, Xue-rui Environmental Science & Technology, Vol. 49, Issue 11 https://doi.org/10.1021/es5049804	journal	May 2015
Aerobic degradation of BDE-209 by Enterococcus casseliflavus: Isolation, identification and cell changes during degradation process Tang, Shaoyu; Yin, Hua; Chen, Shuona Journal of Hazardous Materials, Vol. 308 https://doi.org/10.1016/j.jhazmat.2016.01.062	journal	May 2016
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 10 https://doi.org/10.1093/bioinformatics/btp157	journal	March 2009
Sphingobium fuliginis HC3: A Novel and Robust Isolated Biphenyl- and Polychlorinated Biphenyls-Degrading Bacterium without Dead-End Intermediates Accumulation Hu, Jinxing; Qian, Mingrong; Zhang, Qian PLOS ONE, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pone.0122740	journal	April 2015
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies Wang, Dapeng; Zhang, Yubin; Zhang, Zhang Genomics, Proteomics & Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1016/S1672-0229(10)60008-3	journal	March 2010
New mechanisms of bacterial arsenic resistance Yang, Hung-Chi; Rosen, Barry P. Biomedical Journal, Vol. 39, Issue 1 https://doi.org/10.1016/j.bj.2015.08.003	journal	February 2016
Microbial Bioleaching of Ag, Au and Cu from Printed Circuit Boards of Mobile Phones Díaz-Martínez, María E.; Argumedo-Delira, Rosalba; Sánchez-Viveros, Gabriela Current Microbiology, Vol. 76, Issue 5 https://doi.org/10.1007/s00284-019-01646-3	journal	February 2019
Versatile and open software for comparing large genomes Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L. Genome Biology, Vol. 5, Issue 2, R12 https://doi.org/10.1186/gb-2004-5-2-r12	journal	January 2004
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Laslett, Dean; Canback, Bjorn Nucleic Acids Research, Vol. 32, Issue 1, p. 11-16 https://doi.org/10.1093/nar/gkh152	journal	January 2004
Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China Liu, Jun; Chen, Xi; Shu, Hao-yue Environmental Pollution, Vol. 235 https://doi.org/10.1016/j.envpol.2017.12.008	journal	April 2018
The role of Proteus mirabilis cell wall features in biofilm formation Czerwonka, Grzegorz; Guzy, Anna; Kałuża, Klaudia Archives of Microbiology, Vol. 198, Issue 9 https://doi.org/10.1007/s00203-016-1249-x	journal	June 2016
Characterization of the enhancement of zero valent iron on microbial azo reduction Fang, Yun; Xu, Meiying; Wu, Wei-Min BMC Microbiology, Vol. 15, Issue 1 https://doi.org/10.1186/s12866-015-0419-3	journal	April 2015
Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins Rodgers, Kenton R.; Lukat-Rodgers, Gudrun S. Journal of Inorganic Biochemistry, Vol. 99, Issue 4 https://doi.org/10.1016/j.jinorgbio.2005.02.016	journal	April 2005
P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes Barakat, Mohamed; Ortet, Philippe; Whitworth, David E. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-269	journal	January 2013
ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments Zhang, Zhang; Xiao, Jingfa; Wu, Jiayan Biochemical and Biophysical Research Communications, Vol. 419, Issue 4 https://doi.org/10.1016/j.bbrc.2012.02.101	journal	March 2012
Autecological properties of soil sphingomonads involved in the degradation of polycyclic aromatic hydrocarbons Cunliffe, Michael; Kertesz, Michael A. Applied Microbiology and Biotechnology, Vol. 72, Issue 5 https://doi.org/10.1007/s00253-006-0374-x	journal	March 2006
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1 Wang, Juanping; Wang, Chang; Li, Jionghui Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02238	journal	September 2018
Horizontal Gene Transfer in Prokaryotes: Quantification and Classification Koonin, Eugene V.; Makarova, Kira S.; Aravind, L. Annual Review of Microbiology, Vol. 55, Issue 1 https://doi.org/10.1146/annurev.micro.55.1.709	journal	October 2001
Bacterial Exopolysaccharide mediated heavy metal removal: A Review on biosynthesis, mechanism and remediation strategies Gupta, Pratima; Diwan, Batul Biotechnology Reports, Vol. 13 https://doi.org/10.1016/j.btre.2016.12.006	journal	March 2017
Genome sequence analysis of Cronobacter phage PF-CE2 and proposal of a new species in the genus Pseudotevenvirus Xiao, Mengshi; Ren, Xinmiao; Yu, Ying Archives of Virology, Vol. 166, Issue 12 https://doi.org/10.1007/s00705-021-05255-z	journal	October 2021
CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics Vesth, Tammi; Lagesen, Karin; Acar, Öncel PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0060120	journal	April 2013
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae Journal of Molecular Biology, Vol. 428, Issue 4 https://doi.org/10.1016/j.jmb.2015.11.006	journal	February 2016
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins Tsirigos, Konstantinos D.; Elofsson, Arne; Bagos, Pantelis G. Bioinformatics, Vol. 32, Issue 17 https://doi.org/10.1093/bioinformatics/btw444	journal	September 2016
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
PHASTER: a better, faster version of the PHAST phage search tool Arndt, David; Grant, Jason R.; Marcu, Ana Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw387	journal	May 2016
Environmental contamination from electronic waste recycling at Guiyu, southeast China Leung, Anna; Cai, Zong Wei; Wong, Ming Hung Journal of Material Cycles and Waste Management, Vol. 8, Issue 1 https://doi.org/10.1007/s10163-005-0141-6	journal	March 2006
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 10 https://doi.org/10.1093/bioinformatics/btp157	journal	March 2009
Pseudomonas aeruginosa PAO1 exopolysaccharides are important for mixed species biofilm community development and stress tolerance Periasamy, Saravanan; Nair, Harikrishnan A. S.; Lee, Kai W. K. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00851	journal	August 2015
Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide Tabata, Michiro; Ohhata, Satoshi; Nikawadori, Yuki DNA Research, Vol. 23, Issue 6 https://doi.org/10.1093/dnares/dsw041	journal	August 2016
Gene Amplification and Adaptive Evolution in Bacteria Andersson, Dan I.; Hughes, Diarmaid Annual Review of Genetics, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-genet-102108-134805	journal	December 2009
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Darling, A. C. E. Genome Research, Vol. 14, Issue 7 https://doi.org/10.1101/gr.2289704	journal	June 2004
Sphingobium hydrophobicum sp. nov., a hydrophobic bacterium isolated from electronic-waste-contaminated sediment Chen, Xingjuan; Wang, Haiji; Xu, Jingjing International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 10 https://doi.org/10.1099/ijsem.0.001287	journal	October 2016
Phthalate esters contamination in soil and plants on agricultural land near an electronic waste recycling site Ma, Ting Ting; Christie, Peter; Luo, Yong Ming Environmental Geochemistry and Health, Vol. 35, Issue 4 https://doi.org/10.1007/s10653-012-9508-5	journal	December 2012
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison Richter, Michael; Rosselló-Móra, Ramon; Oliver Glöckner, Frank Bioinformatics, Vol. 32, Issue 6 https://doi.org/10.1093/bioinformatics/btv681	journal	November 2015
Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways Verma, Helianthous; Kumar, Roshan; Oldach, Phoebe BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-1014	journal	January 2014
E-Waste Recycling: Where Does It Go from Here? Zhang, Kai; Schnoor, Jerald L.; Zeng, Eddy Y. Environmental Science & Technology, Vol. 46, Issue 20 https://doi.org/10.1021/es303166s	journal	October 2012
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets Bertelli, Claire; Laird, Matthew R.; Williams, Kelly P. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx343	journal	May 2017
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity Wang, Y.; Tang, H.; DeBarry, J. D. Nucleic Acids Research, Vol. 40, Issue 7 https://doi.org/10.1093/nar/gkr1293	journal	January 2012
Genes under positive selection in Escherichia coli Petersen, L.; Bollback, J. P.; Dimmic, M. Genome Research, Vol. 17, Issue 9 https://doi.org/10.1101/gr.6254707	journal	July 2007
E-Waste Recycling: Where Does It Go from Here? Zhang, Kai; Schnoor, Jerald L.; Zeng, Eddy Y. Environmental Science & Technology, Vol. 46, Issue 20 https://doi.org/10.1021/es303166s	journal	October 2012
Bacterial communities degrading amino- and hydroxynaphthalene-2-sulfonates Nörtemann, B.; Baumgarten, J.; Rast, H. G. Applied and Environmental Microbiology, Vol. 52, Issue 5 https://doi.org/10.1128/aem.52.5.1195-1202.1986	journal	November 1986
Genes under positive selection in Escherichia coli Petersen, L.; Bollback, J. P.; Dimmic, M. Genome Research, Vol. 17, Issue 9 https://doi.org/10.1101/gr.6254707	journal	July 2007
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro Molecular Biology and Evolution, Vol. 34, Issue 8 https://doi.org/10.1093/molbev/msx148	journal	April 2017
Study of the Degradation Activity and the Strategies to Promote the Bioavailability of Phenanthrene by Sphingomonas paucimobilis Strain 20006FA Coppotelli, Bibiana M.; Ibarrolaza, Agustin; Dias, Romina L. Microbial Ecology, Vol. 59, Issue 2 https://doi.org/10.1007/s00248-009-9563-3	journal	July 2009
CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics Vesth, Tammi; Lagesen, Karin; Acar, Öncel PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0060120	journal	April 2013
Horizontal Gene Transfer in Prokaryotes: Quantification and Classification Koonin, Eugene V.; Makarova, Kira S.; Aravind, L. Annual Review of Microbiology, Vol. 55, Issue 1 https://doi.org/10.1146/annurev.micro.55.1.709	journal	October 2001
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA García-Romero, Inmaculada; Pérez-Pulido, Antonio J.; González-Flores, Yolanda Elisabet BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2411-1	journal	February 2016
Carotenoids Play a Positive Role in the Degradation of Heterocycles by Sphingobium yanoikuyae Liu, Xiaorui; Gai, Zhonghui; Tao, Fei PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0039522	journal	June 2012
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins Tsirigos, Konstantinos D.; Elofsson, Arne; Bagos, Pantelis G. Bioinformatics, Vol. 32, Issue 17 https://doi.org/10.1093/bioinformatics/btw444	journal	September 2016
Decolorization of bromoamine acid by a newly isolated strain of Sphingomonas xenophaga QYY and its resting cells Qu, Yuanyuan; Wang, Jing; Zhou, Jiti Biochemical Engineering Journal, Vol. 27, Issue 2 https://doi.org/10.1016/j.bej.2005.08.005	journal	December 2005
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
Role and mechanism of cell-surface hydrophobicity in the adaptation of Sphingobium hydrophobicum to electronic-waste contaminated sediment Chen, Xingjuan; Song, Da; Xu, Jingjing Applied Microbiology and Biotechnology, Vol. 102, Issue 6 https://doi.org/10.1007/s00253-017-8734-2	journal	February 2018
Bacterial resistances to toxic metal ions - a review Silver, Simon Gene, Vol. 179, Issue 1 https://doi.org/10.1016/s0378-1119(96)00323-x	journal	January 1996
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae Journal of Molecular Biology, Vol. 428, Issue 4 https://doi.org/10.1016/j.jmb.2015.11.006	journal	February 2016
Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation Gan, Han; Hudson, André O.; Rahman, Ahmad Yamin BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-431	journal	January 2013

Similar Records

Comparative genomic analysis of nine Sphingobium strains: Insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

Journal Article · 2014 · BMC Genomics · OSTI ID:1223126

Verma, Helianthous; Kumar, Roshan; Oldach, Phoebe; +4 more

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data

Journal Article · 2013 · The ISME Journal · OSTI ID:1623765

Sangwan, Naseer; Verma, Helianthous; Kumar, Roshan; +6 more

The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway

Journal Article · 2012 · Genome Biology and Evolution · OSTI ID:1045862

Copley, Shelley D; Rokicki, Joseph; Turner, Pernilla; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Sphingobium
electronic waste (e-waste)
xenobiotic degradation
heavy metal resistance
comparative genomics
genome plasticity
adaptive evolution

Title: Adaptive Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River Sediment

Citation Formats

References (97)

Similar Records

Related Subjects

Title: Adaptive Evolution of Sphingobium hydrophobicum C1^T in Electronic Waste Contaminated River Sediment