Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage

Abstract

Potato (Solanum tuberosum) is an important staple crop worldwide, it has been cultivated in the Andean Altiplano under low-input farming practices at high altitudes and under harsh environment for centuries. We analyzed secondary metabolite (SM) gene diversity encoded in the potato rhizosphere microbiome during plant growth at three distinct sites located in the Andes at high altitudes by 454-pyrosequencing of non-ribosomal peptide and polyketide biosynthetic genes. Phylogenetic analysis indicated that the majority of rhizosphere SM-encoding sequences differed from previously known sequences and may have distinct ancestors. In particular, actinobacterial methyl-malonyl-CoA transferase and acyl carrier protein from Firmicutes, both involved in the synthesis of SMs, showed widespread distribution of clades which were clearly distinct from sequences deposited in public databases, and only 11% of these sequences could be linked to the production of specific classes of SMs. Although the same cultivar was analyzed, SM gene composition radically differed among plant growth stages and across sites, suggesting a distinct repertoire of SM genes that likely encode diverse SM structures. Also, great diversity of non-ribosomal peptide and polyketide biosynthetic pathways in potato-associated microbiomes in the Andean highlands may represent a rich source of novel natural products.

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture

“…Taxonomic analysis showed that in both the rhizosphere and rhizoplane, the relative abundance of Actinobacteria was significantly lower in MI and Firmicutes was significantly lower in MU and MI when compared with NP ( Figure 3 ). This is in line with previous findings where members of Firmicutes and Actinobacteria were consistently associated with pathogen antagonism and soil disease suppression [ 31 , 32 , 33 ]. Xiong et al [ 28 ] compared microbial communities in suppressive- and conducive-soils associated with Fusarium wilt disease and found that Actinobacteria and Firmicutes were strongly enriched in the suppressive soil in a vanilla long-term continuous cropping system.…”

Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?

“…Especially, we found the seed-associated microbiome could be a reservoir and supplement of secondary metabolic capabilities, in addition to the host plant genome. Just as Aleti et al found, the secondary metabolite genes encoded by potato rhizosphere microbiomes were diverse and vary with the different samples and vegetation stage, which influence on the growth and metabolism of the host plant [ 70 ]. Our study suggested that some core taxa of seed microbiome not only promoted seed germination and plant growth, but also regulated and participated in the secondary metabolism of host plants.…”

The contribution of plant microbiota to economy growth

“…This 'biosynthetic dark matter' can now be accessed by high throughput sequencing techniques and have high potential to provide a number of novel lead structures and compounds (Katz and Baltz, 2016). Due to adaptation to different host niches, differences in the chemical composition of plant hosts and the intense interaction with other microorganisms on and in plants, the plant microbiome provides a hotspot of specific and diverse metabolic and enzymatic potential of microorganisms (Aleti et al, 2017;Hassani et al, 2018). Indeed, sequence comparison within Firmicutes has revealed an enrichment of genomic clusters responsible for secondary metabolite production particularly in those strains, which have been found in association with plants (Aleti et al, 2015).…”