Literature DB >> 31378834

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

Suman Yadav1, Bhaskar Reddy1, Suresh Kumar Dubey2.   

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.

Entities:  

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

Mesh:

Substances:

Year:  2019        PMID: 31378834     DOI: 10.1007/s10142-019-00704-0

Source DB:  PubMed          Journal:  Funct Integr Genomics        ISSN: 1438-793X            Impact factor:   3.410


  53 in total

1.  Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing.

Authors:  Stephanie A Eichorst; Cheryl R Kuske
Journal:  Appl Environ Microbiol       Date:  2012-01-27       Impact factor: 4.792

2.  OrthoANI: An improved algorithm and software for calculating average nucleotide identity.

Authors:  Imchang Lee; Yeong Ouk Kim; Sang-Cheol Park; Jongsik Chun
Journal:  Int J Syst Evol Microbiol       Date:  2015-11-09       Impact factor: 2.747

Review 3.  The potential of cellulases and cellulosomes for cellulosic waste management.

Authors:  Edward A Bayer; Raphael Lamed; Michael E Himmel
Journal:  Curr Opin Biotechnol       Date:  2007-04-25       Impact factor: 9.740

4.  [Cellulolytic activity in various forest soils].

Authors:  E Kiffer; F Mangenot
Journal:  Ann Inst Pasteur (Paris)       Date:  1968-10

5.  Genomic potential for polysaccharide deconstruction in bacteria.

Authors:  Renaud Berlemont; Adam C Martiny
Journal:  Appl Environ Microbiol       Date:  2015-02       Impact factor: 4.792

6.  Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects.

Authors:  Cécile Hervé; Artur Rogowski; Anthony W Blake; Susan E Marcus; Harry J Gilbert; J Paul Knox
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-09       Impact factor: 11.205

7.  Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.

Authors:  Natalia Ivanova; Alexei Sorokin; Iain Anderson; Nathalie Galleron; Benjamin Candelon; Vinayak Kapatral; Anamitra Bhattacharyya; Gary Reznik; Natalia Mikhailova; Alla Lapidus; Lien Chu; Michael Mazur; Eugene Goltsman; Niels Larsen; Mark D'Souza; Theresa Walunas; Yuri Grechkin; Gordon Pusch; Robert Haselkorn; Michael Fonstein; S Dusko Ehrlich; Ross Overbeek; Nikos Kyrpides
Journal:  Nature       Date:  2003-05-01       Impact factor: 49.962

8.  Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.

Authors:  Ana Conesa; Stefan Götz; Juan Miguel García-Gómez; Javier Terol; Manuel Talón; Montserrat Robles
Journal:  Bioinformatics       Date:  2005-08-04       Impact factor: 6.937

9.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Authors:  Marnix H Medema; Kai Blin; Peter Cimermancic; Victor de Jager; Piotr Zakrzewski; Michael A Fischbach; Tilmann Weber; Eriko Takano; Rainer Breitling
Journal:  Nucleic Acids Res       Date:  2011-06-14       Impact factor: 16.971

10.  The RAST Server: rapid annotations using subsystems technology.

Authors:  Ramy K Aziz; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko
Journal:  BMC Genomics       Date:  2008-02-08       Impact factor: 3.969

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  1 in total

1.  Structured Framework and Genome Analysis of Magnaporthe grisea Inciting Pearl Millet Blast Disease Reveals Versatile Metabolic Pathways, Protein Families, and Virulence Factors.

Authors:  Bhaskar Reddy; Sahil Mehta; Ganesan Prakash; Neelam Sheoran; Aundy Kumar
Journal:  J Fungi (Basel)       Date:  2022-06-09
  1 in total

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