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.

中文翻译：

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从土壤中分离出的克雷伯菌 PGPB 促进大麦生长的基因组鉴定

背景

PGPR 已替代化肥以增强土壤的营养成分。尽管编码 PGP 活性的基因存在于 PGPB 中，但它们的活性会随着条件的变化而变化。

客观的

研究三种克雷伯氏菌菌株的比较基因组学及其对体外和土壤条件的反应 PGPR 活性。

方法

我们评估了三种克雷伯氏菌的活性。在两种不同的条件下，特定的缺氮 MS 培养基和温室实验。应用比较基因组学，从三个菌株的全基因组测序中鉴定出编码 PGP 性状的基因。在 RAST 工具包和功能注释的帮助下，确定了编码细胞壁被膜、氮代谢、硫基因和许多其他功能组的基因总数。在blast循环基因组的帮助下，表示了GC含量、假基因和tRNA之间的相似性。SSN1 的基因相似性百分比是针对 M5a1 和 SGM81 的 BLAST 生成的。应用同线性比对和直系同源基因簇等其他方法来了解三个菌株中存在的同源性。

结果

与其他两个菌株相比，SSN1 积极生产最大量的氨 10.97 ± 0.29 µmol/mL。K. oxytoca M5a1 被认为对除产氨以外的所有 PGP 性状都是阴性的。SSN1 的活性在两种条件下均显示出一致的模式，而 M5a1 仅在体外条件下具有活性。编码尿囊素代谢的基因allD、allC、allB、allA、allE、allR、allH在 SSN1 和 M5a1 中被鉴定，但在 SGM81 中不存在。SGM81 和 SSN1 共享最高的 COG，预测最大数量的相似基因。尼夫_基因簇与 M5a1 菌株 98% 相同。

结论

相比之下，SSN1 表达了多种 PGP 性状的附加基因，这表明菌株在缺氮胁迫中的效率更高。