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2015 Annual Science Report

SETI Institute Reporting  |  JAN 2015 – DEC 2015

Biomarker Profiling Using the Life Detector Chip (LDChip)

Project Summary

We have worked on the detection of molecular biomarkers in three relevant environments: Dry (Atacama), acidic (Río Tinto) and deep lake sediments (Andean lakes). Samples have been analyzed in situ by using a powerful biomarker detection chip with and antibody microarray sensor as well in the laboratory with other geomicrobiological tools.

4 Institutions
3 Teams
0 Publications
1 Field Site
Field Sites

Project Progress

By leveraging the 2015 LITA (Life In The Atacama) ASTEP project campaign a set of 90 samples was collected in Atacama desert for analysis. These samples were analyzed both in situ and in the laboratory with a immunological Life Detector Chip (LDChip), ion chromatography (IC), XRD, and biochemical extraction (in progress). In the field the LDChip detected cyanobacteria as well as other bateria and these results were confirmed in the laboratory. The IC profiles indicated the presence of anions that may be critical for certain microbial metabolisms, such as acetate and formate (electron donors) or sulfate and nitrate as electron acceptor for sulfate and nitrate reducing bacteria. The XRD analysis showed the presence of phyllosilicates as well gypsum containing samples.

In order to expand the LDChip capabilities, we have developed new antibodies to three cyanobacterial strains of the Chroococcidiopsis genus. A new collaboration with Dr. Daniela Billi (University of Rome “Tor Vergata”, Italy) provided us the biomass to use as immunogen from three Chroococcidiopsis spp., isolated from extremely arid environments: the Negev and Sinai deserts ad the Antarctic Dry Valleys. The Antibodies have been characterized individually, showing sensitivities at the level 500-1000 cells per mL. As expected, there are strong crossreactions between the Chroococcidiopsis Abs, which indicates that we have redundancy. These new antibodies strengthen the LDChip for in situ detection of cyanobacterial markers by including strains characteristics of hyper arid sites.

Figure 1. shows one of the results obtained after analyzing a sample from Atacama desert (top images) with LDChip. A 0.5 g sample from 80 cm depth collected during LITA2015 campaign was extracted by sonication in 2.5 mL of extraction buffer, filtered through 5 microns and incubated with LDChip with 150 antibodies.
Figure 1. shows one of the results obtained after analyzing a sample from Atacama desert (top images) with LDChip. A 0.5 g sample from 80 cm depth collected during LITA2015 campaign was extracted by sonication in 2.5 mL of extraction buffer, filtered through 5 microns and incubated with LDChip with 150 antibodies. After a second incubation with fluorescent antibodies, and scanning for fluorescence, an image was obtained where bright spots (red over black) correspond to positive detection with the corresponding antibodies (green rectangles). In this case microbial biomarkers from bacteria (Halothiobacillus spp., Salinibacter spp, Streptomyces spp), cyanobacteria, and some archaea such as Halorubrum spp, were detected. LDChip is a powerful technique because it doesn’t need purification procedures such as DNA extraction or enzymatic treatment, which makes it an excellent tool for biomarker detection in environmental monitoring and planetary exploration.

  • PROJECT INVESTIGATORS:
    Victor Parro García Victor Parro García
    Project Investigator
  • PROJECT MEMBERS:
    Daniela Billi
    Collaborator

  • RELATED OBJECTIVES:
    Objective 5.3
    Biochemical adaptation to extreme environments

    Objective 6.1
    Effects of environmental changes on microbial ecosystems

    Objective 7.1
    Biosignatures to be sought in Solar System materials