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NASA NTRS2011

PMA-PhyloChip DNA Microarray to Elucidate Viable Microbial Community Structure

Since the Viking missions in the mid-1970s, traditional culture-based methods have been used for microbial enumeration by various NASA programs. Viable microbes are of particular concern for spacecraft cleanliness, for forward contamination of extraterrestrial bodies (proliferation of microbes), and for crew health/safety (viable pathogenic microbes). However, a "true" estimation of viable microbial population and differentiation from their dead cells using the most sensitive molecular methods is a challenge, because of the stability of DNA from dead cells. The goal of this research is to evaluate a rapid and sensitive microbial detection concept that will selectively estimate viable microbes. Nucleic acid amplification approaches such as the polymerase chain reaction (PCR) have shown promise for reducing time to detection for a wide range of applications. The proposed method is based on the use of a fluorescent DNA intercalating agent, propidium monoazide (PMA), which can only penetrate the membrane of dead cells. The PMA-quenched reaction mixtures can be screened, where only the DNA from live cells will be available for subsequent PCR reaction and microarray detection, and be identified as part of the viable microbial community. An additional advantage of the proposed rapid method is that it will detect viable microbes and differentiate from dead cells in only a few hours, as opposed to less comprehensive culture-based assays, which take days to complete. This novel combination approach is called the PMA-Microarray method. DNA intercalating agents such as PMA have previously been used to selectively distinguish between viable and dead bacterial cells. Once in the cell, the dye intercalates with the DNA and, upon photolysis under visible light, produces stable DNA adducts. DNA cross-linked in this way is unavailable for PCR. Environmental samples suspected of containing a mixture of live and dead microbial cells/spores will be treated with PMA, and then incubated in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.

Venkateswaran, Kasthuri J.↗
NASA NTRS2001

Visualization of Microbial Biomarkers by Scanning Electron Microscopy

We are developing tools to link the biochemical structure of selected biomarkers with putative biogenic structures observed in mineralized samples. The detection of evidence of life on Mars and other planets will rely on methods that can discriminate compounds formed exclusively by living organisms. While biogenic compounds, such as amino acids and nucleotides have been discovered in extraterrestrial sources, such as meteorites and comets, their formation can be explained by abiotic means. The formation of cellular structures, or more elaborate organic molecules, such as complex lipids, proteins or nucleic acids, however, is strongly correlated to the presence of even the most primitive life processes. Recent evidence lends support to the hypothesis that life may have once existed on Mars. Carbonate globules and ppm concentrations of polycyclic aromatic hydrocarbons (PAHs) have been described in ALH84001, a meteorite originating from Mars ejecta captured by Earth over 13,000 years ago. The localized high concentration of PAHs that follow an increasing gradient from the intact fusion crust towards the interior corresponds to microgram quantities of hydrocarbon. Even though ALH84001 and other similar meteorites have withstood the forces capable of ejecting rock through Mars' escape velocity, upon entering Earth's atmosphere, their core temperatures are likely not to have been raised significantly, as evidenced by the survival of remanent magnetic signatures. Ideal biomarkers of ancient or modern biological life would include molecules that are (or were) pervasive and highly resistant to degradation. Also, requisite methods of detection should be simple, extremely sensitive and broadly inclusive (NASA SP-530). Lipopolysaccharide (LPS), peptidoglycan or pseudopeptidoglycan and beta-glucan are microbial cell wall components which together cover the entire microbial spectrum of eubacteria, archea and fungi. They are all remarkably resistant to thermal degradation. Fortunately, many antimicrobial defense systems of higher organisms require sensitive detection to combat microbial pathogens. We employ here the primitive immune system of the evolutionarily ancient horseshoe crab, Limulus polyphemus. This species relies on multi-enzyme signal amplification detection of cell wall molecules and they can be applied to the development of useful detectors of life. An extension of this work includes the visualization of microbial signatures by labeling LAL components with chromogenic or electron dense markers. The protein Limulus Anti-LPS Factor (LALF) has an extremely high affinity for LPS. By coupling LALF binding with colloidal gold labels we demonstrate a correlation of the structures visible by electron microscopy with biochemical evidence of microbial cell wall materials. Pure silica particles were mixed with cultures of E. coli (10(exp 6) cfu/mL). Samples were washed sequentially with buffered saline, LALF, antibody to LALF and finally colloidal gold-labeled Protein A. Negative controls were not exposed to E. coli but received identical treatment otherwise. Samples were coated with carbon and imaged on a JEOL JSM-840 scanning electron microscope with LaB6 source in the back scatter mode with the JEOL annular back scatter detector. 20 nm-scale black spots in this contrast-reversed image originate from electrons back-scattered by gold atoms. Negative controls did not give any signal. Future work will expand application of this technique to soil simulants and mineralized rock samples.

Wainwright, Norman R.↗
NASA NTRSDate not supplied

Olivine Dissolution and Formation of Secondary phases in Ultramafic Soils

Introduction: Olivine has been proposed as an indicator for the duration of water-rock interaction within Martian rocks and sediments [1-3]. The use of olivine as a mineralogical indicator for past aqueous alteration on Mars requires interpretation of a complex combination of factors including pH, temperature, and composition [5,6]. Here, we examine the persistence of natural olivine within terrestrial ultramafic soils (Fe/Mg-rich, Al-poor) developing under different climatic conditions and the incipient dissolution of emplaced forsterite (Fo) and fayalite (Fa) surfaces to investigate environmental effects on incipient olivine dissolution, olivine persistence in soils, and formation of secondary phases. Methods: Field Sites. We examined olivine weathering and secondary material formation in ultramafic soils at 6 sites in the Klamath Mountains (KM) of northern California with a mean annual temperature of ~12.8℃ and precipitation of ~55.7-95.4 cm/year [7], and soil pH of ~6.5-7.3; 4 sites in the Tablelands (TB) of Newfoundland, Canada with a mean annual temperature of <3.9℃ and precipitation of ~120.0 cm/year [8], and soil pH of ~7.7; and at 3 sites at Pickhandle Gulch (PG), Nevada with a mean annual temperature of ~14.4℃ and precipitation of ~14.1 cm/year [7], and soil pH of ~8.5. Sampling sites span an age range of ~12.1-50+ kya in the Klamath Mountains [9,10] and ~13-30 kya in the Tablelands [11]. Pickhandle Gulch sites are undated. Parent Material and Soil Analyses. Polished thin sections of bulk soil prepared by Wagner Petrographic, Inc were carbon-coated and analyzed on a JEOL 2100 SEM in back-scattered electron mode in the EMIL lab at UNLV and at the 13-ID-E synchrotron beamline at Argonne National Laboratory using µXRF, µXRD, and XAS. Soil and parent material samples were powdered in a Fritsch pulverisette and analyzed by XRD and soil by VNIR. Soil preparation is further described in [12]. Disk Preparation, Burial, and Collection. Fo disks were cut from a column prepared via hot-pressing and Fa disks by sintering synthetic fayalite powder, see [13] for detail. Disks were polished to a 0.25-micron level with diamond grit. Disks were buried in 3 KM soils, 4 TB soils, and 3 PG soils, collected after exactly 365 days, and washed gently with 100% reagent grade ethanol to remove potential adhered soil material. Weathered disks and soil samples were stored in a -20℃ freezer until analysis. Unaltered control disks prepared identically to the buried disks were stored at -20℃ for the duration of the experiment. Disk Analyses. One Fo and Fa disk from each climate zone was analyzed on a variable pressure Zeiss Supra 40VP SEM at Northern Arizona University. A separate Fo and Fa disk from each climate zone was analyzed by XPS using a Physical Electronics VersaProbe II at the Penn State Univ. Materials Characterization Lab after a Na-dodecyl sulfate wash and ozonation to remove carbon contamination as in [14]. VNIR measurements were conducted at Johnson Space Center using an ASD FieldSpec3 under ambient lab conditions on a separate Fo and Fa disk from each climate zone. One separate Fo and Fa control sample was analyzed for each technique for comparison with weathered samples. XPS uncertainty was determined from 5 repeat measurements on controls. Results: Bedrock and Soil Results Olivine is present in the parent material in the KM and TB. Olivine is found in ~12.1 ka KM soils but is absent from all older soils, while persisting into the oldest (>20 ka) TB soil (Figure 1). In both locations, olivine is found as cores surrounded by a serpentine rind (Figure 2). VNIR spectra from the analyzed soils possess strong OH-associated spectral features at ~2.33 µm indicating the presence of Mg-rich phyllosilicates as well as ferric-oxide features at ~0.92 µm in the KM (Figure 3). Primary crystalline silicate grains mostly incorporate Fe2+, while poorly crystalline weathering rinds are best fit by ferric oxide XAS standards (Figure 4). µXRF also shows that Fe and Ni concentrate in weathering rinds and Cr remains within interior silicate grains (Figure 4). Buried Sample Results All Fo surfaces exhibited formation of dissolution features including shallow pitting not observed on controls. Dissolution features were most visually widespread on the KM disk (Figure 5). Leaching of Mg from KM and TB Fo disks was evident from <1.6 Mg/Si ratios measured by XPS (Figure 6). Fe-rich precipitates in SEM (Figure 5) and Fe presence in XPS scans (Figure 6) indicate Fe deposition onto KM and TB Fo disk surfaces. The appearance of a spectral feature at 0.55 µm in the VNIR spectra from the TB Fo suggests this Fe is ferric (Figure 7). The PG Fo appears least altered, with minimal formation of dissolution features in SEM (Figure 5), a Mg/Si ratio inconsistent with leaching (~2) (Figure 6), and VNIR spectra almost identical to the control sample. Analysis of Fa surfaces is ongoing. The higher temperatures and more acidic pH in the KM soils likely drive the faster dissolution of the Fo disks described above. While the TB soils experience greater precipitation than in the KM, the cooler temperatures and more basic soil pH facilitate observable but more limited alteration. The dry climate and basic soil pH at PG lead to minimal dissolution of the PG disk surfaces.

A D Feldman↗