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Functional & Integrative Genomics

, Volume 20, Issue 1, pp 89–101 | Cite as

De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils

  • Suman Yadav
  • Bhaskar Reddy
  • Suresh Kumar DubeyEmail author
Original Article
  • 116 Downloads

Abstract

Cellulose, the most abundant polysaccharide in nature, is a rich source of renewable energy and sustains soil nutrients. Among the microorganisms known to degrade cellulose, bacteria are less studied compared to fungi. In the present work, we have investigated the culturable bacteria actively involved in cellulose degradation in forest and crop field soils. Based on clear zone formation and enzyme activity assay, we identified 7 bacterial strains positive for cellulose degradation. Of these, two most efficient strains (Bacillus cereus strains BHU1 and BHU2) were selected for whole genome sequencing, annotation, and information regarding GC content, number of genes, total subsystems, starch, and cellulose degradation pathways. Average nucleotide identity (ANI) showed more than 90% similarity between both the strains (BHU1 and BHU2) and with B. cereus ATCC 14579. Both the strains have genes and enzyme families like endoglucanase and β-glucosidase as evident from whole genome sequence. Cellulase containing gene families (GH5, GH8, GH1), and many other carbohydrate-degrading enzymes, were present in both the bacterial strains. Taken together, the results suggest that the strains were efficient in cellulose degradation, and can be used for energy generation and production of value-added product.

Keywords

Crop and forest soils Bacillus cereus Cellulase De novo genome assembly GH family 

Notes

Acknowledgments

We also thank Coordinator CAS, DST-FIST, and PURSE for facilities.

Funding information

One of the authors (Suman) is grateful to CSIR, New Delhi, India, for the financial assistance in the form of Junior and Senior Research Fellowship.

Compliance with ethical standards

Conflict of interest

Authors have no any conflict of interest for this publication

Supplementary material

10142_2019_704_MOESM1_ESM.doc (74 kb)
Fig. S1 Starch and sucrose metabolic pathway of B. cereus BHU1 and BHU2 strain. Green colored boxes show the presence of ECs in both the isolates while yellow color boxes reveal the absence of ECs in BHU2 strain (DOC 74 kb)
10142_2019_704_MOESM2_ESM.xlsx (85 kb)
Table S1 Subsystem and InterPro annotation of B. cereus BHU1 and BHU2 strains (XLSX 84 kb)

References

  1. Ayres E, Steltzer H, Berg S, Wall DH (2009) Soil biota accelerate decomposition in high-elevation forests by specializing in the breakdown of litter produced by the plant species above them. J Ecol 97:901–912Google Scholar
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75PubMedPubMedCentralGoogle Scholar
  3. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477PubMedPubMedCentralGoogle Scholar
  4. Barras F, Boyer MH, Chambost JP, Chippaux M (1984) Construction of a genomic library of Erwinia chrysanthemi and molecular cloning of cellulase gene. Mol Gen Genet 197(3):513–514Google Scholar
  5. Bayer EA, Lamed R, Himmel ME (2007) The potential of cellulases and cellulosomes for cellulosic waste management. Curr Opin Biotechnol 18(3):237–245PubMedGoogle Scholar
  6. Berg B, Laskowski R (2006) Litter decomposition: a guide to carbon and nutrient turnover. Academic Press, AmsterdamGoogle Scholar
  7. Bergey DH, Holt JG (1994) Bergey’s manual of determinative bacteriologyGoogle Scholar
  8. Berlemont R, Martiny AC (2015) Genomic potential for polysaccharide deconstruction in bacteria. Appl Environ Microbiol 81:1513–1519PubMedPubMedCentralGoogle Scholar
  9. Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T (2013) antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41:W204–W212PubMedPubMedCentralGoogle Scholar
  10. Boer W, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29(4):795–811PubMedGoogle Scholar
  11. Brumm PJ (2013) Bacterial genomes: what they teach us about cellulose degradation. Biofuels 4:669–681Google Scholar
  12. Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59–60PubMedGoogle Scholar
  13. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676PubMedPubMedCentralGoogle Scholar
  14. DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE (2008) Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol 190(15):5455–5463PubMedPubMedCentralGoogle Scholar
  15. Eichorst SA, Kuske CR (2012) Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Appl Environ Microbiol 78(7):2316–2327PubMedPubMedCentralGoogle Scholar
  16. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A (2011) CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 6:11PubMedPubMedCentralGoogle Scholar
  17. Gao B, Jin M, Li L, Qu W, Zeng R (2017) Genome sequencing reveals the complex polysaccharide-degrading ability of novel deep-sea bacterium Flammeovirga pacifica WPAGA1. Front Microbiol 8:600PubMedPubMedCentralGoogle Scholar
  18. Ghose T (1987) Measurement of cellulase activities. Pure Appl Chem 59:257–268Google Scholar
  19. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57(Pt 1):81–91Google Scholar
  20. Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181–W184PubMedPubMedCentralGoogle Scholar
  21. Hatami S, Alikhani H, Besharati H, Salehrastin N, Afrousheh M, Yazdani Z, Jahromi Z (2008) Investigation on aerobic cellulolytic bacteria in some of north forest and farming soils. Am Eurasian J Agric Environ Sci 3(5):713–716Google Scholar
  22. Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G (1995) Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases. Proc Natl Acad Sci U S A 92(15):7090–7094PubMedPubMedCentralGoogle Scholar
  23. Herve C, Rogowski A, Blake AW, Marcus SE, Gilbert HJ, Knox JP (2010) Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects. Proc Natl Acad Sci U S A 107(34):15293–15298PubMedPubMedCentralGoogle Scholar
  24. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423(6935):87–91PubMedGoogle Scholar
  25. Kameshwar AK, Qin W (2016) Recent developments in using advanced sequencing technologies for the genomic studies of lignin and cellulose degrading microorganisms. Int J Biol Sci 12(2):156–171PubMedPubMedCentralGoogle Scholar
  26. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28(1):27–30PubMedPubMedCentralGoogle Scholar
  27. Kiffer E, Mangenot F (1968) Cellulolytic activity in various forest soils. Ann l’Inst Pasteur 115(4):582–595Google Scholar
  28. Kim D, Ku S (2018) Bacillus cellulase molecular cloning, expression, and surface display on the outer membrane of Escherichia coli. Molecules 23(2):503PubMedCentralGoogle Scholar
  29. Koeck DE, Pechtl A, Zverlov VV, Schwarz WH (2014) Genomics of cellulolytic bacteria. Curr Opin Biotechnol 29:171–183PubMedGoogle Scholar
  30. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874Google Scholar
  31. Ladomersky E, Petris MJ (2015) Copper tolerance and virulence in bacteria. Metallomics 7:957–964PubMedPubMedCentralGoogle Scholar
  32. Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66(2):1100–1103PubMedPubMedCentralGoogle Scholar
  33. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495PubMedGoogle Scholar
  34. Lopez-Mondejar R, Zuhlke D, Becher D, Riedel K, Baldrian P (2016) Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 6:25279PubMedPubMedCentralGoogle Scholar
  35. Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, DiBartolo G, Martinez M, Lapidus A, Lucas S, Copeland A, Richardson P, Wilson DB, Kyrpides N (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol 189(6):2477–2486PubMedPubMedCentralGoogle Scholar
  36. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66(3):506–577PubMedPubMedCentralGoogle Scholar
  37. Malan TP, Kolb A, Buc H, McClure WR (1984) Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter. J Mol Biol 180(4):881–909PubMedGoogle Scholar
  38. Maya K, Singh RS, Upadhyay SN, Dubey SK (2011) Kinetic analysis reveals bacterial efficacy for biodegradation of chlorpyrifos and its hydrolyzing metabolite TCP. Process Biochem 46(2):2130–2136Google Scholar
  39. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346PubMedPubMedCentralGoogle Scholar
  40. Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31(3):426–428Google Scholar
  41. Mols M, de Been M, Zwietering MH, Moezelaar R, Abee T (2007) Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics. Environ Microbiol 9(12):2933–2944PubMedGoogle Scholar
  42. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33:201–205Google Scholar
  43. Nacke H, Engelhaupt M, Brady S, Fischer C, Tautzt J, Daniel R (2012) Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes. Biotechnol Lett 34:663–675PubMedGoogle Scholar
  44. Nema N, Alamir L, Mohammad M (2015) Production of cellulase from bacillus cereus by submerged fermentation using corn husks as substrates. Int Food Res J 22(5):1831–1836Google Scholar
  45. Park T, Seo S, Shin T, Cho BW, Cho S, Kim B, Lee S, Ha JK, Seo J (2018) Molecular cloning, purification, expression, and characterization of β-1, 4-endoglucanase gene (Cel5A) from Eubacterium cellulosolvens sp. isolated from Holstein steers’ rumen. Asian Australas J Anim Sci 31(4):607–615PubMedGoogle Scholar
  46. Patagundi BI, Shivasharan C, Kaliwal B (2014) Isolation and characterization of cellulase producing bacteria from soil. Int J Curr Microbiol Appl Sci 3(5):59–69Google Scholar
  47. Perez J, Munoz-Dorado J, de la Rubia T, Martinez J (2002) Biodegradation and biological treatments of cellulose, hemicellulose and lignin: an overview. Int Microbiol 5(2):53–63PubMedGoogle Scholar
  48. Robson LM, Chambliss GH (1984) Characterization of the cellulolytic activity of a Bacillus isolate. Appl Environ Microbiol 47(5):1039–1046PubMedPubMedCentralGoogle Scholar
  49. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425PubMedGoogle Scholar
  50. Sootsuwan K, Thanonkeo P, Keeratirakha N, Thanonkeo S, Jaisil P, Yamada M (2013) Sorbitol required for cell growth and ethanol production by Zymomonas mobilis under heat, ethanol, and osmotic stresses. Biotechnol Biofuels 6:180PubMedPubMedCentralGoogle Scholar
  51. Stursova M, Zifcakova L, Leigh MB, Burgess R, Baldrian P (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80(3):735–746PubMedGoogle Scholar
  52. Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43(4):777–780PubMedPubMedCentralGoogle Scholar
  53. Thayer DW, David CA (1978) Growth of “seeded” cellulolytic enrichment cultures on mesquite wood. Appl Environ Microbiol 36:291–296PubMedPubMedCentralGoogle Scholar
  54. Todorov SD (2009) Bacteriocins from Lactobacillus plantarum—production, genetic organization and mode of action: produção, organização genética e modo de ação. Braz J Microbiol 40(2):209–221PubMedPubMedCentralGoogle Scholar
  55. Waldrop MP, Zak DR, Sinsabaugh RL, Gallo M, Lauber C (2004) Nitrogen deposition modifies soil carbon storage through changes in microbial enzymatic activity. Ecol Appl 14(4):1172–1177Google Scholar
  56. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697–703PubMedPubMedCentralGoogle Scholar
  57. Whitfield C, Paiment A (2003) Biosynthesis and assembly of Group 1 capsular polysaccharides in Escherichia coli and related extracellular polysaccharides in other bacteria. Carbohydr Res 338(23):2491–2502PubMedGoogle Scholar
  58. Whittle DJ, Kilburn DG, Warren RA, Miller RC Jr (1982) Molecular cloning of a Cellulomonas fimi cellulose gene in Escherichia coli. Gene 17(2):139–145PubMedGoogle Scholar
  59. Wirth S, Ulrich A (2002) Cellulose-degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil. Syst Appl Microbiol 25(4):584–591PubMedGoogle Scholar
  60. Woo HL, Hazen TC, Simmons BA, DeAngelis KM (2014) Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Syst Appl Microbiol 37(1):60–67PubMedGoogle Scholar
  61. Yan S, Wu G (2013) Secretory pathway of cellulase: a mini-review. Biotechnol Biofuels 6:177PubMedPubMedCentralGoogle Scholar
  62. Yang JK, Zhang JJ, Yu HY, Cheng JW, Miao LH (2014) Community composition and cellulase activity of cellulolytic bacteria from forest soils planted with broad-leaved deciduous and evergreen trees. Appl Microbiol Biotechnol 98(3):1449–1458PubMedGoogle Scholar
  63. Zdobnov EM, Apweiler R (2001) InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17(9):847–848PubMedGoogle Scholar
  64. Zeng R, Xiong P, Wen J (2006) Characterization and gene cloning of a cold-active cellulase from a deep-sea psychrotrophic bacterium Pseudoalteromonas sp. DY3. Extremophile 10(1):79–82Google Scholar
  65. Zhang W, Li Z, Miao X, Zhang F (2009) The screening of antimicrobial bacteria with diverse novel nonribosomal peptide synthetase (NRPS) genes from South China Sea sponges. Mar Biotechnol (New York, NY) 11(3):346–355Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Suman Yadav
    • 1
  • Bhaskar Reddy
    • 1
  • Suresh Kumar Dubey
    • 1
    Email author
  1. 1.Laboratory of Molecular Ecology, Centre of Advanced Study in Botany, Institute of ScienceBanaras Hindu UniversityVaranasiIndia

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