Sheetal Sharma1, Shraddha Gang2, Jorg Schumacher3, Martin Buck2, Meenu Saraf4. 1. Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India. 2. Department of Life Science, Faculty of Natural Sciences, Imperial College, London, SW7 2AZ, UK. 3. Department of Life Science, Faculty of Natural Sciences, Imperial College, London, SW7 2AZ, UK. j.schumacher@imperial.ac.uk. 4. Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India. sarafmeenu@gmail.com.
Abstract
BACKGROUND: PGPR has substituted chemical fertilizers to enhance the nutrient profile of the soil. Although gene encoding for PGP activity is present in PGPB their activity changes in response to conditions. OBJECTIVE: To study comparative genomics for three Klebsiella strains and their PGPR activity in response to in vitro and soil condition. METHODS: We evaluated the activity of three Klebsiella spp. in two different conditions, specific nitrogen-deficient MS media and greenhouse experiment. Applying comparative genomics, genes encoding for PGP traits were identified from the whole-genome sequencing of the three strains. With the help of the RAST tool kit and functional annotation, a total number of genes encoding for cell wall capsule, nitrogen metabolism, sulfur genes and many other functional groups were identified. With the help of blast circular genome, similarity between GC content, pseudogene and tRNA was represented. The percentage of gene similarity of SSN1 was generated against BLAST with M5a1 and SGM81. Other methods like synteny alignment and orthologous gene clusters were applied to understand the homologous present in three strains. RESULTS: SSN1 was actively producing the maximum amount of ammonia 10.97 ± 0.29 µmol/mL compared to the other two strains. K. oxytoca M5a1 was considered negative for all PGP traits except ammonia production. The activity of SSN1 was showing a consistent pattern both the conditions whereas M5a1 was only active in vitro condition. Gene encoding for allantoin metabolism allD, allC, allB, allA, allE, allR, allH were identified in SSN1 and M5a1 but was absent in SGM81. The highest COG was shared between SGM81 and SSN1 predicting a maximum number of similar genes. The nif gene cluster was 98 % identical to the M5a1 strain. CONCLUSIONS: Comparatively, SSN1 expressed the additional gene for various PGP traits which suggest higher efficiency of strain in nitrogen deficiency stress.
BACKGROUND: PGPR has substituted chemical fertilizers to enhance the nutrient profile of the soil. Although gene encoding for PGP activity is present in PGPB their activity changes in response to conditions. OBJECTIVE: To study comparative genomics for three Klebsiella strains and their PGPR activity in response to in vitro and soil condition. METHODS: We evaluated the activity of three Klebsiella spp. in two different conditions, specific nitrogen-deficient MS media and greenhouse experiment. Applying comparative genomics, genes encoding for PGP traits were identified from the whole-genome sequencing of the three strains. With the help of the RAST tool kit and functional annotation, a total number of genes encoding for cell wall capsule, nitrogen metabolism, sulfur genes and many other functional groups were identified. With the help of blast circular genome, similarity between GC content, pseudogene and tRNA was represented. The percentage of gene similarity of SSN1 was generated against BLAST with M5a1 and SGM81. Other methods like synteny alignment and orthologous gene clusters were applied to understand the homologous present in three strains. RESULTS: SSN1 was actively producing the maximum amount of ammonia 10.97 ± 0.29 µmol/mL compared to the other two strains. K. oxytoca M5a1 was considered negative for all PGP traits except ammonia production. The activity of SSN1 was showing a consistent pattern both the conditions whereas M5a1 was only active in vitro condition. Gene encoding for allantoin metabolism allD, allC, allB, allA, allE, allR, allH were identified in SSN1 and M5a1 but was absent in SGM81. The highest COG was shared between SGM81 and SSN1 predicting a maximum number of similar genes. The nif gene cluster was 98 % identical to the M5a1 strain. CONCLUSIONS: Comparatively, SSN1 expressed the additional gene for various PGP traits which suggest higher efficiency of strain in nitrogen deficiency stress.
Authors: Alka Gupta; Murali Gopal; George V Thomas; Vinu Manikandan; John Gajewski; George Thomas; Somasekar Seshagiri; Stephan C Schuster; Preeti Rajesh; Ravi Gupta Journal: PLoS One Date: 2014-08-27 Impact factor: 3.240