Deconstructing complexity in microbial communities by molecular fingerprinting
Most microbial communities are very complex. With considerable effort (and enough money!) it may be possible
to identify most microbes from a community. This activity would involve culturing, cloning, sequencing,
metagenomics, pyrosequencing, FISH, etc. However, microbial communities are virtually infinite combinations of species
and relative abundances. Even worse, microbial diversity changes fast and significantly across
time and space. Monitoring such changes in many samples by repeated sequencing is not worth doing
if molecular fingerprints can be established for the different strains identified in a community. Other applications of fingerprinting include: tracking specific microbes, identifying sources of contamination and
hosts of pathogens, and monitoring mixed cultures and microcosms. To achieve such goals libraries of fingerprints have
to be constructed, methods have to be used that are reproducible and have high phylogenetic resoution and laboratory protocols
have to be very accurately described. At PSU we optimize fingerprinting conditions, construct libraries of molecular fingerprints of important phylogroups, and use them to monitor changes in microbial
diversity.
Olivine respiration by iron-oxidizers and signatures of life on Mars
Olivine is a mineral found in volcanic rocks. As a semiprecious stone the name of olivine is "peridote".
Microscopic analysis of thin sections of olivine crystals showed the presence of microchannels 0.5-10 microns in diameter
in some olivine crystals. In the last few years such microchannels were found in 3 billion years old rocks and in the
Martian meteorite Nakhla. But, were these microchannels made by life? Some micro-tunnels appear to be made abiotically
(dissolution in acid water, ... some microchannel-like features are in fact decorated incrustations). Yet, some microchannels
are believed to be made by microbes. We propose that microchannels in olivine crystals can also be made by iron-oxidizing
microbes. We isolate such microbes, study their physiology and the mechanisms they use do obtain iron from olivine and
to weather the crystal lattice, and the signatures they leave in olivine crystals.
Magnetism, H217O and the Origin of Biochiraliy
All amino acids from proteins are L-enantiomers while ribose
and deoxyribose form RNA and DNA are D-enantiomers. Though the benefits of biochirality are more or less clear,
its origin is very hard to explain. Life could not have started without large chiral disruption, yet large chiral disruption
was very unlikely during prebiotic evolution. We propose that the origin of large prebiotic chirality resulted from
a combination of two factors: (1) Symmetry breaking (due to the effect of some specific laws of our universe being
asymmetric); and (2) Chiral amplification (due to entropy decrease in energy dissipative chemical systems).
We study the chemical asymmetry induced by the Zeeman Effect and Lorentz Force on spin-enantiomers. Our chemical models
are chiral monomers interacting with H217O in magnetic fields. We measure enantio-differences
in proton exchange parameters using Time Domain 1H Nuclear Magnetic Resonance (Scorei et al., 2007). This research program
is a collaboration between Romulus. I. Scorei and Vily M. Cimpoiasu at University of Craiova (Romania), and Radu Popa at Portland
State University (Portland, OR, USA).
