Microbial Ecology and Environmental applications


Alejandro Caro-Quintero

Graduate Student , Biology Department, University of Puerto Rico at Mayaguez Campus


Research Interests


Microbial diversity and function of disturbed environments; Development of aerobic and anaerobic culturing techniques coupled to molecular biology to select degrading consortia; Implementation of bioinformatic tools that relates microbial diversity data with ecological hypothesis testing.


Download Scripts for TRFLP Analysis  PEAKS, BINNING

Download CLISP-2.38



 Research Experience

January 2003 – June 2004. Hydrocarbon Bioremediation and Microbial Heavy Metal Resistance. Center of Microbial Investigations (CIMIC)  -Link

June 2005 – July 2005.  Jim C. Spain Laboratory, Georgia Institute of Technology -Link

August 2004 – to the present. Tropical Microbial Ecology Laboratory. Supervisor: Dr. Arturo Massol, Ph.D  -Link


  Microbial Community Structure Analysis

Figure 1. Vieques (east manuver area) soil and marine sediment microcosms amended with explosives (RDX and 2,4 DNT).


Figure 2. An example of an acrylamide gel with terminal restriction fragments generated by digesting ribosomal RNA genes  with RsaI, MspI, and HaeIII. Each band represent  an OTU (Operational Taxonomic Unit).


Figure 3. Detrented Correspondance Analysis  (DCA) of T-RFLP profiles used to assess the  environmental variables that drives a microbial community shift.


Figure 4. Heatmap Analysis of T-RFLP profiles used to identify potential degrading- OTU's.

Biology M.S.Candidate,2005-2007

(University of Puerto Rico)


Military training areas, such as the AFWTF of Vieques Island, are potential sites for finding novel explosive degrading microorganisms due to the historical use of large amounts of munitions and  the great number of UXO’s (Unexploded Ordnance) that persist on soil and marine sediments


Soil and marine sediment aerobic and anerobic  microcosms were separately amended with 2,4-dinitrotoluene (DNT),  and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In order to examine the consequences of the presence of nitroaromatic compounds on the microbial community structure, Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis of the 16S rRNA genes was performed using total DNA extracted from microcosm samples. Explosive and nitrite concentration levels  were mesured to detect a degradation activity (GC and HPLC analysis, and colorimetric method, respectively).  Unexposed systems were used as controls. 


Partial results suggest and unique phylotypes enrichment coupled to RDX and 2,4-DNT degradation in soil microcosms. Correspondence analysis of T-RFLP patterns show that Vieques samples cluster distant from the non-polluted reference location samples. Profiles  corresponding to 2,4-DNT-amended treatments present less variation than unexposed systems, suggesting that 2,4-DNT exhorts a selective pressure which limits microbial community changes. Understanding function and community structure will assist in the development of environmental restoration strategies and prediction of the potential of indigenous microbial communities to face a chemical disturbance.< namespace="" prefix="o" ns="urn:schemas-microsoft-com:office:office" xml="true">

Vieques Island Inclusion in the Superfund National Priorities List. -Link.



-Primer designing and PCR optimization (In situ-, reverse transcription-, real time-, nested-, touchdown-, hot start-, colony- PCR).

-Bioinformatic skills (ClustalW, BioEdit, Primer Select, MegAlign, blast, FastPCR, PHYLIP, DOTUR, ASLO, MEGA).

-Programming Skills (development of scripts to analyse T-RFLP raw data from gel sequencer data, using recursive iteration on LISP language)

-DNA cloning, DNA, RNA and plasmid extractions, gel electrophoresis, enzyme restrictions, DNA sequencing, T-RFLP, FISH)



-Heat Shock proteins. Hypothesis No 3 p. 10-17 (2004). -Link

-Heavy Metal Resistance of DNT Degraders (Georgia Institute of Technology, 2005). -Link




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Laboratory courses (U< namespace="" prefix="st1" ns="urn:schemas-microsoft-com:office:smarttags" xml="true">niversity of Puerto Rico at Mayagüez, 2004- 2007)

BIOL 3010L, Cellular Physiology -Link

BIOL 4365L, Microbial Ecology -Link

Among the practical session improved was the Mineralization of organic matter (OM): Instead of working only with petroleum, the students measured the mineralizations of four different compounds (glucose, sucrose, xylene, and diesel), comparing its mineralization curves in two different type of soils (sandy and organic). Mineralization.doc - Link

CIBI 3031L, Biological Science I -Link