mgPGPT: Metagenomic analysis of plant growth-promoting traits

Abstract

In a recent publication, we introduce the PGPT ontology and PGPT-db of bacterial plant growth-promotion traits and associated database of protein sequences, and provide several tools for bacterial genome analysis on the PLaBAse server. Here, we extend the scope of the PGPT ontology to perform PGPT analysis of metagenomic datasets. First, we introduce mgPGPT-db, an extended database of 39, 582, 183 protein sequences obtained computationally by including proteins from AnnoTree. With this, we have integrated the PGPT ontology into our metagenome analysis tool MEGAN and provide mapping files to identify PGPT-related genes using the results of a DIAMOND alignment of reads against either the new mgPGPT-db database, the NCBI-nr protein database, or the AnnoTree protein database. We demonstrate and compare these different approaches in detail on an example data set and evince the improvement compared to the PGPT-db. We also compare the inferred PGPT content of several samples taken from different environments and reveal plant specific PGPT clustering. IMPORTANCEA deeper understanding of plant growth-promoting traits of bacteria is important to enlight and enhance the native plant-beneficial bacterial functional diversity regarding the environmental stress adaption or the ability to suppress even food-borne pathogens by strain inoculation dedicated to agriculture and other plant production systems. The work presented here extends recent work beyond the analysis of individual to allow the assessment of the PGPT potential of metagenomes obtained from environmental samples.