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