Transcriptome Characteristics Of A Petroleum-degrading L.fusiformis Strain 15-4

The breakthrough in transcriptome research of prokaryotes shows its unique advantage in revealing the molecular mechanism of the life process of prokaryotes.The transcriptome study of prokaryotes began with pathogenic bacteria.In recent years,transcriptome analysis of the degradation mechanism of pollutants by prokaryotes has become a research hotspot.The metabolic mechanism,mechanism of action and transcription-related genes of degrading bacteria were further explored through the integrated analysis of multiple omics.Crude oil pollution has become one of the major environmental problems.In this study,a crude oil degrading bacteria was isolated from the soil in Qinghai-tibet Plateau and was identified as Lysinibacillus fusiformis.Based on the analysis of crude oil degradation,transcriptome analysis was performed to explore the degradation mechanism of the degradation bacteria.Our result will provide basic data for microbial remediation of crude oil contaminated soil in cold region.The main results are as follows.1.A petroleum-degrading bacteria strain was isolated from the soil in the Qinghai-Tibet Plateau.The strain could degrade 56.64%±3.34 of petroleum added in the medium as sole carbon source at 20?.16SrRNA gene sequence alignment shows strain 15-4 has 99%similarity with Lysinibacillus fusiformis.Thus it was designated as Lysinibacillus fusiformis15-4.2.L.fusiformis 15-4,a strain grown on a medium with crude oil as the sole carbon source,was used as the treatment sample?LF?.The strain grown in LB medium was served as control sample?CK?.The samples were taken at the medium of culture logarithm?24 h?.RNA extraction and transcriptome sequencing were performed.Illumina Hiseq^TM 2000platform sequencing generated a total of 14,813,173 reads in the CK sample,of those13,416,919 reads?90.59%?were mapped to the reference genome.A total of 13,519,099reads were obtained in the LF group,of those 12,797,112 reads?94.68%?were mapped to the reference genome.A total of 4,664 genes were annotated from the reads of two sample groups,among them,4658?99.9%?genes can be annotated by Nr database,2758?59.2%?genes were annotated by swiss-prot database,and 3672?78.72%?genes can be annotated by the String database.2587 genes?55.5%?were annotated to at least one GO term,3080?66.1%?genes could be annotated to COG,633?13.6%?genes were annotated to NOG,and 2264?48.6%?genes were annotated to KEGG.Gene expression analysis showed that 3969?85.1%?genes were expressed in the samples,of these,2,239 genes accounting for 56.4%were upregualted,and 1,730 genes accounting for 43.6%were downregulated,.3.COG annotation showed that 3080?66.1%?genes were assigned to 20 COG classifications with the top of amino acid transport,metabolism and signal transduction.GOannotation showed that 2587?55.5%?genes were annotated to 45 GO terms with the top of metabolic process,the cellular process,the catalytic activity,the cell membrane of single-cell biological cells,and the activity of transcription factors.A total of 2264?48.6%?genes were annotated into 169 KEGG pathways with the top of ABC transporters,two-component system,amino acids biosynthesis,and carbon metabolism in a diverse environment.4.The GO enrichment analysis of differentially expressed genes?DEGs?indicates that63.3%?1387?genes were enriched to at lease one GO with the top significant difference?p<0.001?of biological adhesion,multi-organism process reproduction,developmental process,and localization under subcategory biological process,and extracellular region,membrane under cellular component,and nutrient reservoir activity,protein binding transcription factor activity,transport activity,and nucleic acid binding transcription factor activity under subcategory molecular function.The functions of biological adhesion,development,localization of extracellular membrane,nutrient reservoir activity,transcription factor activity,and transport activity were significantly up-regulated in the treatment group.56.6%?1244 DEGs?genes could be annotated into KEGG.The pathways ABC transporter,transporter,lipid metabolism,and transcriptional regulator were highly induced while energy metabolism and translation and protein folding were highly repressed.5.Analysis of DEGs showed that 2192?55.2%?genes were significantly differentially expressed in the treatment group?p<0.001?.All these DEGs can be annotated by the Nr database.67.2%?1474 DEGs?can be annotated by the Swiss-prot database,and 89.9%?1971DEGs?can be annotated by the String database.Among them,1312 DEGs was significantly up-regulated?59.9%?,and 880 DEGs was significantly down-regulated?40.1%?.The genes involved in diverse metabolic pathways were significantly up-regulated by crude oil treatment.These pathways include ABC transporters,a variety of dehydrogenase,two-component system protein,transcription regulators,and environmental response proteins.The utilization of crude oil as carbon source induced the expression of diverse genes involved in hydrocarbon degradation in strain 15-4,suggesting that,at the gene level,this strain showed strong potential of crude oil degradation.