Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72
<i>Sphingobium yanoikuyae</i> S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH))...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-06-01
|
| Series: | Applied Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-3417/12/12/6201 |
| _version_ | 1797490191915548672 |
|---|---|
| author | Eric Sanchez Lopez Temidayo Oluyomi Elufisan Patricia Bustos Claudia Paola Mendoza Charles Alberto Mendoza-Herrera Xianwu Guo |
| author_facet | Eric Sanchez Lopez Temidayo Oluyomi Elufisan Patricia Bustos Claudia Paola Mendoza Charles Alberto Mendoza-Herrera Xianwu Guo |
| author_sort | Eric Sanchez Lopez |
| collection | DOAJ |
| description | <i>Sphingobium yanoikuyae</i> S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil. |
| first_indexed | 2024-03-10T00:28:28Z |
| format | Article |
| id | doaj.art-480f5d7147f244699731bdc6f5bbcc78 |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-10T00:28:28Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Sciences |
| spelling | doaj.art-480f5d7147f244699731bdc6f5bbcc782023-11-23T15:29:32ZengMDPI AGApplied Sciences2076-34172022-06-011212620110.3390/app12126201Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72Eric Sanchez Lopez0Temidayo Oluyomi Elufisan1Patricia Bustos2Claudia Paola Mendoza Charles3Alberto Mendoza-Herrera4Xianwu Guo5Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Boulevard del Maestro/Esq. Elías pina S/N, Reynosa 88710, Tamaulipas, MexicoLaboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Boulevard del Maestro/Esq. Elías pina S/N, Reynosa 88710, Tamaulipas, MexicoCentro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, MexicoLaboratorio Interacción Planta-Microrganismo, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro/Esq. Elías pina S/N, Reynosa 88710, Tamaulipas, MexicoLaboratorio Interacción Planta-Microrganismo, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro/Esq. Elías pina S/N, Reynosa 88710, Tamaulipas, MexicoLaboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Boulevard del Maestro/Esq. Elías pina S/N, Reynosa 88710, Tamaulipas, Mexico<i>Sphingobium yanoikuyae</i> S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.https://www.mdpi.com/2076-3417/12/12/6201naphthalenephenanthreneGC-MSbphenyl<i>Sphingobium</i>toluene |
| spellingShingle | Eric Sanchez Lopez Temidayo Oluyomi Elufisan Patricia Bustos Claudia Paola Mendoza Charles Alberto Mendoza-Herrera Xianwu Guo Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72 Applied Sciences naphthalene phenanthrene GC-MS bphenyl <i>Sphingobium</i> toluene |
| title | Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72 |
| title_full | Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72 |
| title_fullStr | Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72 |
| title_full_unstemmed | Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72 |
| title_short | Complete Genome Report of a Hydrocarbon-Degrading <i>Sphingobium yanoikuyae</i> S72 |
| title_sort | complete genome report of a hydrocarbon degrading i sphingobium yanoikuyae i s72 |
| topic | naphthalene phenanthrene GC-MS bphenyl <i>Sphingobium</i> toluene |
| url | https://www.mdpi.com/2076-3417/12/12/6201 |
| work_keys_str_mv | AT ericsanchezlopez completegenomereportofahydrocarbondegradingisphingobiumyanoikuyaeis72 AT temidayooluyomielufisan completegenomereportofahydrocarbondegradingisphingobiumyanoikuyaeis72 AT patriciabustos completegenomereportofahydrocarbondegradingisphingobiumyanoikuyaeis72 AT claudiapaolamendozacharles completegenomereportofahydrocarbondegradingisphingobiumyanoikuyaeis72 AT albertomendozaherrera completegenomereportofahydrocarbondegradingisphingobiumyanoikuyaeis72 AT xianwuguo completegenomereportofahydrocarbondegradingisphingobiumyanoikuyaeis72 |