Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem

Appl Environ Microbiol. 2016 Jan 8;82(6):1807-1817. doi: 10.1128/AEM.02781-15.

Abstract

Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / classification
  • Archaea / genetics
  • Archaea / isolation & purification*
  • Asteraceae / microbiology*
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Biota*
  • Colombia
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Metabolic Networks and Pathways / genetics*
  • Microarray Analysis
  • Plant Leaves / microbiology*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Soil Microbiology

Substances

  • DNA, Ribosomal
  • RNA, Ribosomal, 16S

Grant support

This work was financed by Colciencias (contract no. 573-2012 and 649-2013) and was performed under MADS contract no. 76-2013 for access to genetic resources and UAESPNN Research permit no. PIDB DTAO 021-10. The funding agencies had no role in study design, data collection and interpretation, or the decision to submit the work for publication.