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.

Figure 1

Phylogenetic tree showing the distribution of PKS sequences from Firmicutes. ACP DNA sequences were clustered at 85% sequence identity and subsequent representative sequences from OTUs were aligned in ClustalW and neighbor-joining tree was displayed in iTOL2. Branches of reference sequences were colored bright red, rhizosphere soil sequences were colored by site (P1, P2 and P3), and outer ring was colored according to plant growth stage (emergence and senescence).

Figure 2

Phylogenetic tree showing the distribution of PKS sequences from Actinobacteria. Representative sequences from OTUs extracted after DNA sequences of KS and met-mal-CoA clustered separately at 85% sequence identity were subjected to multiple sequence alignment by ClustalW and neighbor-joining tree was displayed in iTOL2. Branches of NCBI-nt reference sequences were colored bright red, rhizosphere soil sequences were colored by site (sequences from P1 were colored in light yellow, P2 colored in aqua blue and P3 colored in magenta), and outer ring colored according to vegetation stage (sequences from emergence were colored in coral orange and senescence colored in olive green).

Figure 3

Percentage of secondary metabolite clades shared among vegetation stages and sites. Rhizosphere sequences from three distinct sites (P1, P2 and P3) and two plant developmental stages (emergence and senescence) were clustered at 97, 90 and 85% sequence identity. Percentage of shared and specific clades among sites and vegetation stages were represented in Venn diagrams constructed to appropriate scale.