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Genes possessed by microbes in the rhizosphere influence the metabolic activities that occur in this zone. Although the maize rhizosphere has been reported to be a hotspot of genes, these genes remain under-investigated. Hence, this study aimed at identifying putative microbial genes with plant beneficial functions in the underexplored maize rhizosphere microbiome using a shotgun metagenomics approach. Sampling was done at the flowering stage of the maize plants and both the rhizosphere and bulk soils were collected in triplicates. The metagenomes of the examined rhizosphere and bulk soils revealed genes involved in carbon fixation, nitrogen fixation, iron acquisition, heat and cold shock, phosphorus solubilization and utilization, sulfur cycling, and siderophore production. The beta diversity analysis showed significant variations (p < 0.05) in these genes across the examined rhizosphere and bulk soils which was further confirmed by the distinct separations between the samples as seen on the principal coordinate analysis (PCoA) plot. Contrarily, no significant difference was observed in diversity within the habitats (p = 0.99). The predominance of significant genes of agricultural importance such as the nifH, nifA, groES, and cspA in the rhizosphere metagenomes signifies that this region is endowed with beneficial organisms with potential for improving plant growth, mitigating stress, and reducing the effect of extreme temperatures, which can be optimized in developing biofertilizers. Therefore, the development of strategies that will help in cultivating these organisms, which are mostly unculturable, is encouraged. This would make them readily available for use as bio-inoculants and in other biotechnological applications

In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes our assays revealed novel toxins and restriction enzymes, and new classes of small non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator dnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.

In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes our assays revealed novel toxins and restriction enzymes, and new classes of small non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator dnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.