Metagenomics and Bioprospecting of Microbial_GEBIX_MM

Metagenomics and Bioprospecting of Microbial_GEBIX_MM

Metagenomics and Bioprospecting of Microbial
Communities in the Colombian Andes
María Mercedes Zambrano
www.gebix.org.co
www.corporgen.org
Center for Genomics and Bioinformatics of
Extreme Environments - Gebix
U de Los Andes
U Nacional
U Javeriana
Corpogen
U de Caldas
ParqueSoft
U del Valle
U del Cauca
Biodiversity
Biodiversity in Colombia
•  Mega-diverse (plants/animals)
•  Variety of ecosystems
•  Tropical Andes: “Hotspot” for diversity
Nevados NNP
o  Rela%vely unexplored -­‐ reservoir o  Unique ecosystems /endangered o  Extreme environments (To, water, radia%on) Characterization/ Bioprospecting
metagenomics
⠁ Microbial communties:
16S rRNA analysis (V5 –V6 region)
Metagenomic sequences
⠃ Microbial collections
New species
Enzymes / metabolism
⠇ Metagenomic Libraries
Relative abundance
Initial exploration
S9 - Valle Tumbas
S11 - Suelo glacial
V5-V6 region – 16S rRNA
A8 - Trillizas
A5/10 - Calvario
Analysis - Termal El Coquito
454
Phylochip
10
27
8
16S rRNA
1
o 
o 
o 
o 
o 
3
3
4
Differences among strategies
Libraries
Bacteria >>> Archaea
Novel sequences / microalgea
Similarity with acidic sites
Metabolic diversity (phototrophs/heterotrophs/chemolithotrophs)
Microb Ecol. 2012 Jan;63(1):103-15
Comparative hot spring
analysis
- Geographically close
- Water composition differences
2,500 m – 4, 600m 29oC – 68oC pH: 2-­‐ 7 A1 2.0 57 A4 2.7 A6 2.7 29 30 A5 3.1 35 802 6.5 58 P3 6.9 68 0.06
o  Groups characteristic of each site
o  Clustering - Environmental parameters (pH and Temp)
Delgado, in prep.
Metagenomic analysis of Coquito (A4)
Mesophilic (29oC)
3,973m
Rich in sulfate & iron
Proteobacteria
Taxonomic affilia%on o 
o 
o 
o 
Metabolic routes Xenobiotics
Biodegradation and
Metabolism
Biosynthesis of
Other Secondary
Metabolites
Biosynthesis of
Polyketides and
Terpenoids
Carbohydrate
Metabolism
3000
2500
2000
1500
1000
500
0
Metabolism of
Cofactors and
Vitamins Glycan
Biosynthesis and
Metabolism
Energy Metabolism
Lipid Metabolism
Nucleotide
Metabolism
Amino Acid
Metabolism
Metabolism of
Other Amino Acids
Similar to acidic places / acidophiles
Few phototrophic bacteria (Cyanobacteria); chloroplasts (eukaryotes)
Iron & Sulfur cycling – chemolithotrophs (minerals for E)
Primary production (E y C) – solar energy and inorganic substrates
Jiménez, sub.)
Proteorhodopsins
Light-driven H+ pumps
Membrane proteins
For E production (marine)/ Survival
Widespread
eDNA
PCR
PRs in these acidic springs -  Proton pumping activity
-  Green absorbing proteins
(λmax 525 nm)
o  Community E production:
metals, carbon, sunlight
Appl Environ Microbiol. 2012 Aug 31
Bioprospecting
Actinomycetes
N-fixing microbes
Lipidic substrates - New species
Enzymes – lipases / cellulases
Microbial collec%ons Properties / Physiology
Genomics/ Proteomics, etc
Bioprospecting
Antimicrobial activity
Cells / consortia
Bioprospecting
o  Cellulases
Metagenomic Libraries Arid soils
Glacial
o  Lipases
o  Proteases
!
1st screen
On palm waste
1st screen
!
!
Cloning, expression, characterization
!
World J Microbiol Biotechnol. 2012 28(1):361-70
Antonie Van Leeuwenhoek. 2012 101(2):205-15)
Ardila, in prep
Microbial communities in Andean
ecosystems
Microbial
Diversity
Functionality
Isolates
Bioprospecting
!
!
Gebix Center
Corpogen
Javeriana U
S. Baena, JS Montaña, D Jiménez,
G. López, C Rubiano, D Alvarez, L Bernal
C Osorio, H Junca, L Delgado,
L Bohórquez, C Ruiz, JR
Bustos, JM Anzola
UniAndes
S Restrepo, LM Rodríguez, D
Chaves, A Bernal
U Valle / Cauca
P Vélez, P Moreno
U Nacional
E Torres, MI Chacón, G
Nemogá, O Lizarazo, C
López
ParqueSoft
F Barraza
U del Caldas
LM Alvarez
Thank you
- MAVDT Contract Access to Genetic Resources No.
15-2008
- Resarch permit DTNO-N-20/2007 (UAESPNN)
- Funding: Colciencias & SENA