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