WHOLE GENOME SEQUENCING OF Bacillus altitudinis AGE-B8, A POTENTIAL CELLULOLYTIC BACTERIUM ISOLATED FROM ROTTED SUGAR CANE BAGASSE
Abstract
Bagasse is a major source of lignocellulose that is produced in a huge amount in Egypt. It can be used as a second-generation biofuel starting material, fibers for paper, and substrate for high-value microbial products. The present study describes the isolation of cellulose-degrading bacterial strain, AGE-B8, isolated from rotted sugar cane bagasse. AGE-B8 bacterium was tested for the cellulases induction under various parameters such as pH, incubation temperature, incubation time, carbon sources. The best filter-paper enzyme (FPase) activity was obtained after incubation for 7 days at 34ºC, while best carboxymethyl cellulase (CMCase) activity was obtained after incubation for 7 days at 37ºC. The strain was identified using multilocus sequence analysis as Bacillus altitudinis. A draft assembly of the AGE-B8 genome was performed. The assembly was submitted to NCBI under project number PRJNA675729, BioSample number SAMN16712403, and SRA accession number SRR13084424. A total of 3,540 genes were identified in the produced bacterial genome assembly. Gene annotation and genetic variation analysis was performed for the identified isolate. A detailed list of all mutations, in reference to the NCBI Bacillus altitudinis reference genome, was identified. The results will significantly contribute to a better understanding of the genetics of the lignocellulosic degrading bacteria.
References
Adney B., and J. Nrel B., (1996). Measurement of cellulase activities. In: Laboratory Analytical Procedure No. 006. Golden, CO: National RenewableEnergy Laboratory.
Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhanger W., and Lipman D. J., (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research. 25:.3389-3402. https://doi.org/10.1093/nar/25.17.3389
Aziz R. K., Bartels D., Best A., DeJongh M., Disz T., Edwards R. A., and Zagnitko O., (2008). The RAST Server: Rapid annotations using subsystems technology. BMC Genomics, 9:1-15. https://doi.org/10.1186/1471-2164-9-75
Bolger A. M., Lohse M., and Usadel B., (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30: 2114- 2120.
https://doi.org/10.1093/bioinformatics/btu170
Bradner J. R., Gillings M., and Nevalainen K. M. H., (1999). Qualitative assessment of hydrolytic activities in antarctic microfungi grown at different temperatures on solid media. World Journal of Microbiology and Biotechnology, 15: 143-145. https://doi.org/10.1023/A:1008855406319
Cingolani P., Platts A., Wang L. L., Coon M., Nguyen T., Wang L., and Ruden D. M., (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6: 80-92. https://doi.org/10.4161/fly.19695
Davis J. R., Goodwin L. A., Woyke T., Teshima H., Bruce D., Detter C., and Sello J. K., (2012). Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete. Journal of Bacteriology, (2012): 2396-2397. https://doi.org/10.1128/JB.00186-12
Florencio C., Couri S., and Farinas C. S., (2012). Correlation between agar plate screening and solid-state fermentation for the prediction of cellulase production by trichoderma strains. Enzyme Research, 2012. https://doi.org/10.1155/2012/793708
García-Huante Y., Cayetano-Cruz M., Santiago-Hernández A., Cano-Ramírez C., Marsch-Moreno R., Campos J. E., and Hidalgo-Lara M. E., (2017). The thermophilic biomass-degrading fungus Thielavia terrestris Co3Bag1 produces a hyperthermophilic and thermostable β-1,4-xylanase with exo- and endo-activity. Extremophiles, 21: 175-186. https://doi.org/10.1007/s00792-016-0893-z
Gebbie L., Dam T. T., Ainscough R., Palfreyman R., Cao L., Harrison M., and Speight R., (2020). A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile. BMC Biotechnology, 20: 1-16. https://doi.org/10.1186/s12896-020-00609-y
Ghose T. K., (1987). Measurement of cellulase activities. Pure and Applied Chemistry, 59: 257-268. https://doi.org/10.1351/pac198759020257
Gusakov A. V., (2011). Alternatives to Trichoderma reesei in biofuel production. Trends in Biotechnology,. (9): 419-425. https://doi.org/10.1016/j.tibtech.2011.04.004
Gutierrez-Correa M., and Tengerdy R. P., (1997). Production of cellulase on sugar cane bagasse by fungal mixed culture solid substrate fermentation. Biotechnology Letters, 19: 665-667. https://doi.org/10.1023/A:1018342916095
Kasana R. C., Salwan R., Dhar H., Dutt S., and Gulati A., (2008). A rapid and easy method for the detection of microbial cellulases on agar plates using Gram’s iodine. Current Microbiology, 57: 503-507. https://doi.org/10.1007/s00284-008-9276-8
Kucharska K., Rybarczyk P., Hołowacz I., Łukajtis R., Glinka M. and Kamiński M., (2018). Pretreatment of lignocellulosic materials as substrates for fermentation processes. Molecules, 23: 2937.
Kumar S., Stecher G., and Tamura K., (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 33: 1870-1874. https://doi.org/10.1093/molbev/msw054
Li H., and Durbin R., (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., and Durbin R., (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25:2078-2079. https://doi.org/10.1093/bioinformatics/btp352
Liu Y., Lai Q., Dong C., Sun F., Wang L., Li G., and Shao Z., (2013). Phylogenetic diversity of the Bacillus pumilus group and the marine ecotype revealed by multilocus sequence analysis. PLoS ONE, 8: 1-11. https://doi.org/10.1371/journal.pone.0080097
Luo X., Liu J., Zheng P., Li M., Zhou Y., Huang L., Chen L. and Shuai L., (2019). Promoting enzymatic hydrolysis of lignocellulosic biomass by inexpensive soy protein. Biotechnology for biofuels, 12: 1-13.
Maki M., Leung K. T., and Qin W., (2009). The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. International Journal of Biological Sciences, 5: 500-516. https://doi.org/10.7150/ijbs.5.500
Mhuantong W., Charoensawan V., Kanokratana P.,Tangphatsornruang S., and Champreda V., (2015). Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnology for Biofuels, 8(1). https://doi.org/10.1186/s13068-015-0200-8
Mosier N., Wyman C., Dale B., Elander R., Lee Y. Y., Holtzapple M., and Ladisc M., (2005). Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresource Technology, 96: 673-686. https://doi.org/10.1016/j.biortech.2004.06.025
Ohta Y., Nishi S., Kobayashi K., Tsubouchi T., Iida K., Tanizaki A., and Hatada Y., (2015). Draft genome sequence of Novosphingobium sp. strain MBES04, isolated from sunken wood from Suruga Bay, Japan. Genome Announcements, 3(1). https://doi.org/10.1128/genomeA.01373-14
Pandey A., Soccol C. R., Nigam P., and Soccol V. T., (2000). Biotechnological potential of agro-industrial residues. I: Sugarcane bagasse. Bioresource Technology, 74: 69-80. https://doi.org/10.1016/S0960-8524(99)00142-X
Pham J. V., Yilma M. A., Feliz A., Majid M.T., Maffetone N., Walker J. R., Kim E., Cho H. J., Reynolds J. M., Song M. C. and Park S. R., (2019). A review of the microbial production of bioactive natural products and biologics. Frontiers in microbiology, 10: 1404.
Prabhakaran M., Couger M. B., Jackson C. A., Weirick T., and Fathepure B. Z., (2016). Genome sequences of the lignin-degrading Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r isolated from decaying wood. Genome Announcements, 3(2). https://doi.org/10.1128/genomeA.00019-15
Rattanachomsri U., Kanokratana P., Eurwilaichitr L., Igarashi Y., and Champreda V., (2011). Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles. Bioscience, Biotechnology and Biochemistry, 75: 232-239. https://doi.org/10.1271/bbb.100429
Rubin E. M., (2008). Genomics of cellulosic biofuels. Nature, 454(7206): 841-845. https://doi.org/10.1038/nature07190
Saitou N., and Nei M., (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4: 406-425. https:// doi.org/10.1093/oxfordjournals.mo lbev.a040454
Seemann T., (2014). Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30: 2068-2069. https://doi.org/10.1093/bioinformatics/btu153
Shi Y., Chai L., Tang C., Yang Z., Zhang H., Chen R., and Zheng Y., (2013). Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8. Biotechnology for Biofuels, 6(1). https://doi.org/10.1186/1754-6834-6-1
Teather R. M. and P. Wood J., (1982). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Applied and Environmental Microbiology, 43: 777-780. https://doi.org/10.1128/aem.43.4.777-780.1982
Vega K., Villena G. K., Sarmiento V. H., Ludeña Y., Vera N., and Gutiérrez- Correa M., (2012). Production of Alkaline Cellulase by Fungi Isolated from an Undisturbed Rain Forest of Peru. Biotechnology Research International, 2012: 1-7. https://doi.org/10.1155/2012/934325
Wang L. T., Lee F. L., Tai C. J., and Kasai H., (2007). Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. International Journal of Systematic and Evolutionary Microbiology, 57: 1846-1850. https://doi.org/10.1099/ijs.0.64685-0
Woo H. L., Ballor N. R., Hazen T. C., Fortney J. L., Simmons B., Davenport K. W., and DeAngeisK. M., (2014a). Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Standards in Genomic Sciences, 9(1): 19. https://doi.org/10.1186/1944-3277-9-19
Woo H. L., Utturkar S., Klingeman D., Simmons B. A., DeAngelis K. M., Brown S. D., and Hazen T. C., (2014b). Draft genome sequence of the lignin-degrading Burkholderia sp. strain LIG30, isolated from wet tropical forest soil. Genome Announcements, 2(3). https://doi.org/10.1128/genomeA.00637-14
Youseif S. H., Abd El-Megeed F. H., Ageez A., Cocking E. C., and Sale S. A., (2014). Phylogenetic multilocus sequence analysis of native rhizobia nodulating faba bean (Vicia faba L.) in Egypt. Systematic and Applied Microbiology, 37: 560-569. https://doi.org/10.1016/j.syapm.2014.10.001
Youseif Sameh H, El-megeed F. H. A., Mohamed A. H., Ageez A., Veliz E., and Martínez-romero E., (2021). Diverse Rhizobium strains isolated from root nodules of Trifolium alexandrinum in Egypt and symbiovars. Systematic and Applied Microbiology, 44(1): 126156. https://doi.org/10.1016/j.syapm.2020.126156.
