Dr Randall S Perry

Listed below is a selection of past and current abstracts.



Accumulation and deposition of inorganic and organic compounds by microcolonial fungi


Randall S. Perry1, Anna Gorbushina2, Michael H. Engel3, Vera M. Kolb4, Wolfgang E. Krumbein2, and James T. Staley5


1Department of Earth and Space Sciences, University of Washington, Seattle, Washington 98195-1310 USA


2Geomicrobiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany


3 School of Geology and Geophysics, University of Oklahoma, Norman, Oklahoma 73019 USA


4Department of Chemistry, University of Wisconsin-Parkside, Kenosha, Wisconsin 53141-2000 USA


5 Department of Microbiology and Immunology, School of Medicine, University of Washington, Seattle, Washington 98195-1310 USA


A seemingly unique feature of desert varnish is its worldwide association with microcolonial fungi (MCF). The surface environments on rock coatings are some of the most hostile on Earth. High temperatures, low humidity, high incidence of UV light and low nutrients require microorganisms that have evolved special survival skills. MCF’s contain melanin, microsporines, carotinoids and probably other as yet unidentified pigments that help protect them from UV light. They are chemoorganatrophs deriving their nutrients from aeolian deposits from pollen (found using SEM)), plant residue such as Eugenol (see below), other bio chemicals delivered to their surfaces and also by microorganisms, bacteria, or actinomycetes  that die in the shelter of the larger MCF (ca 100µm and larger). Large amounts of exopolymeric substances are produced by the colonies. MCF becomes coated with detritus and perhaps the encrustation of these grains and mineral plates is also a protective mechanism. Small wind-blown clay platelets can be oriented by polysaccharides and may provide additional protection from solar energy.  It is also possible that the physical nature of the spherical clusters provide a protective mechanism. The fungal colonies grow very slowly over dozens to hundreds of years, and because of their capacity to survive the desert-surface-rock conditions, are often the only seemingly viable inhabitants of arid and  alpine rocks. While the colonies are slow growing, they eventually die and subsequently degrade. Younger colonies have less mineral concentrations and were analyzed using scanning electron microscopy (SEM) with x-ray mapping and EDS. Generally the elemental composition other then carbon and nitrogen, of young colonies is O > Si > Al > Ca and lesser amounts of Mg >K > Na > Fe > Mn. The idea that MCF and black yeast microcolonies degrade and become part of rock coatings is supported by SEM micrographs  presented here.  Older colonies appear to become more mineral rich.  As the colonies  become part of rock coatings the organic and inorganic constituents might also be preserved.  Mycosporine-like amino acids, frequently possessed by cyanobacteria are present in MCF. DNA sequencing of the varnish rock coatings confirms the presence of Cyanobacteria. It has been suggested that spectral changes of rock surfaces that are usually attributed to metal oxidation of iron and manganese might also be staining by microbially produced organic and inorganic pigment absorbed polymers on rock surfaces or in coatings.  In order to test the idea that MCF become part of coatings, we analyzed desert varnish from the Mojave Desert using time-of-flight secondary ion mass spectroscopy (TOF-SIMS). Several polyfunctional chemicals in the coatings were found such as Eugenol, but melanin and other MCF compounds have not yet been identified. SEM and EDS analysis confirm the presence of clay like particles on MCF. The clays of varnish surfaces and surrounding soils were separated and then analyzed using XRD. Soil samples contained kaolinite, smectite and trace cholorite. Surprisingly, varnish samples had only trace aounts of smectite and contained illite and kaolinite. Given the large amount of smectite in soils, one would expect to find it in the varnish coatings. Treatment with glycerol expands a peak at 11.3 degrees to ca 8-10 degrees. Heating to 550ºC removes this peak and also would remove organic peaks. A layered hydroxide would react this way and the d-spacing is suggestive of a layered hydroxide such as pyroaurite or hydrotalcite rather then kaolinite and smectite interstratified layers. Hydrated birnessite might expand similarily but the d-spacing is a bit large (7.8 A).  Fungal polysaccharides may form stable organomineral complexes with some clays.  EPS substances from MCF might also bind with clays, metal oxides or amorphous silica. This accumulation of inorganic substances mixed with organic compounds may be preserved in rock coatings and provide unique chemical markers. Rock varnish coatings may exist on Mars and might sequester evidence of past or present life. Understanding how fungi such as MCF protect themselves from UV, dehydration, and temperature extremes and subsequently become part of mineral coatings, provides an interesting possible analogue for detection of past or present life on Mars.




Biological and organic constituents of desert varnish: review and new hypotheses

 


Randall S. Perry *(1) and Vera M. Kolb(2)


 


(1) Department of Earth and Space Sciences, Astrobiology Center for Early Evolution,

Box 351310, University of Washington, Seattle, Washington 98195-1310


 (2) Department of Chemistry, University of Wisconsin-Parkside, Kenosha, Wisconsin 53141-2000


 


ABSTRACT

 


Desert varnish coatings are found on rock surfaces throughout arid regions of the world.  Rock varnishes may exist on Mars, as suggested by some observations on both Viking and Mars Pathfinder landing sites.  There has long been a debate as to whether varnish coatings are microbially mediated or deposited by inorganic processes.  Dozens of bacteria have been cultured from the surface of varnish coatings and recently the molecular ecology of varnish coatings have been characterized using 16S rRNA techniques.  Colonies of micro colonial fungus are associated with varnish coatings but it is unclear whether bacteria or fungi are directly involved in varnish formation. Re-examination of a ten-year-old in vitro experiment to grow varnish-using bacteria cultured from varnish surfaces provides some answers and is useful in designing new lab experiments.  Another alternative is the incorporation of microbial components into varnish coatings either by complexation with metals or in association with clays or silica.  For instance, polysaccharides found in bacterial cell walls contain linear polymers of sugars that may be preserved in arid conditions when complexed with usual varnish components such as calcium, aluminum, silicon, iron and manganese.  Understanding the organic components of desert varnish may help to resolve the question of the mechanism of formation of rock coatings, biomineralization processes, and bacterial fossilization and how to detect past microbial activity on planets.


Keywords:  Desert varnish, rock coatings, silicic acid, amino acids, DNA, Microcolonial fungi




Preliminary identification of fullerenes in lowermost Jurassic strata, Queen Charlotte Islands, British Columbia



Randall S. Perry*(a), James W. Haggart (b), Peter D. Warda


(a) Department of Earth and Space Sciences, Box 351310, University of Washington, Seattle, WA 98195-1310 USA


(b) Geological Survey of Canada, 101-605 Robson Street, Vancouver, BC V6B 5J3 Canada


 Abstract


The Triassic-Jurassic (TJ) mass extinction (~200 mya) event is one of the most severe in geologic history.  It is also one of the most poorly understood.  Few geologic sections containing the TJ boundary interval have been identified globally, and most of those are poorly preserved; the paucity of suitable stratigraphic sections has prevented corroborative geochemical studies of this interval.  Recently, fullerene molecules (C60 to C200) have been shown to be present in the mass extinction boundary intervals of the Permian-Triassic (PT) event (~251.4 mya), as well as the well-known “dinosaur” extinction event of the Cretaceous-Tertiary (KT) (~65 mya).  The presence of fullerenes in both these extinction intervals has been used to invoke an extraterrestrial impact cause for the extinctions. Preliminary results of laser desorption mass spectrometry (LDMS) of selected samples from the Kennecott Point TJ boundary section, Queen Charlotte Islands, British Columbia, suggest that fullerenes (C60 to ~C200) are present in the section, stratigraphically above the extinction interval (as defined by paleontological and isotopic data), but not actually within the interval itself.  The presence of fullerenes may not be diagnostic of an impact event.


Keywords: Jurassic, Triassic/Jurassic Boundary, fullerenes, Queen Charlotte Islands, impact events




Biochemical markers in rock coatings



Randall S. PERRY (1) and Vera M. KOLB (2)


 (1) Department of Earth and Space Science


 University of Washington, Seattle WA 98195-1310, USA


 (2) Department of Chemistry


 University of Wisconsin- Parkside, Kenosha, WI 53141-2000, USA


Abstract. Rock coatings are ubiquitous in arid regions of the world. We have measured amino acids in desert varnish coatings and considered other organic compounds as chemical biosignatures in coatings. Understanding the mechanisms of formation or rock coatings and identifying their active and fossil biosignatures will provide useful methods for contrasting biotic and abiotic systems on Earth and other planetary bodies.


From Darwin to Mars: desert varnish as a model for preservation of complex (bio)chemical systems


Randall S. Perry (1)* and Vera M. Kolb (2)*


(1) Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195-1310  2Department of Chemistry, University of Wisconsin-Parkside, Kenosha, WI 53141-2000


The search for life on Mars is an important goal of NASA and other space agencies. It is not known if chemical evolution on Mars produced the same or similar types of life as on Earth.  If not, what would non-Earth biosignatures look like?  If life has left its footprint on Mars, what chemical signatures can we recognize, and how can we prevent missing novel life signatures? Alternatively, chemical evolution on Mars may have produced complex chemical systems, which, however, did not lead to life.  How can such systems be identified?  We use as a model a complex inorganic-organic-biotic system on Earth, commonly called desert or rock varnish, which has been known to Darwin, and which is now also indicated on Mars.  We describe unique complex chemical markers that are preserved in rock varnish on Earth.  An intricate interaction between minerals, metals, and organic compounds is responsible for their preservation.  We suggest some important types of organic compounds to look for in the Martian varnish, should it exist.


Keywords: definition of life, transition zone, chemical evolution, desert varnish, rock varnish, chemicals in the varnish, organosilicates, silicic acid, alternative genetic systems


(1) Michael H. Engel and (2) Randall S. Perry


 


(1) School of Geology & Geophysics


100 East Boyd Street


The University of Oklahoma, Norman, Oklahoma 73019 USA


 


(2) Randall S. Perry, Department of Earth and Space Sciences


University of Washington, Seattle, Washington 98195


On Earth, organic matter is found in association with sediments and sedimentary rocks.  Sedimentary rocks that have undergone slight to moderate metamorphism may also contain remnants of organic matter incorporated prior to deformation.  Igneous rocks, however, may only contain organic matter if it is introduced via fluid migration into fractures subsequent to crystallization.  The Martian meteorites collected to date are all igneous rocks.  Thus, the chances that they contain indigenous organic matter, biotic or abiotic, are remote.  Whether the organic material in fractures of ALH84001 is indigenous or is contamination resulting from an extended residence time on Earth prior to collection, remains unresolved.  What is clear, however, is that the current collection of Martian meteorites is far from ideal with respect to determining the types of organic compounds that may have been incorporated into sediments on the Martian surface.  Carbonaceous meteorites consist of material derived from the solar nebula 4.5 billion years ago.  They also exhibit varying degrees of aqueous processing thought to have occurred on a parent body(s) in the region of the asteroid belt during the early stages of formation of the solar system.   Life appears to have existed on Earth for as far back in time as the rock record extends (~3.8 Ga).  Thus, the only record for the solar system organic inventory that preceded life’s origin on Earth or Mars are carbonaceous meteorites.  In particular, the CI and CM carbonaceous meteorites contain many of the building blocks for life as we know it.  It is interesting to note, however, that of the twenty protein amino acids common to all organisms, only eight have been observed in carbonaceous meteorites.  A hypothesis is presented to account for the absence of the remaining twelve amino acids that are essential for life and how their presence or absence can be used to determine if life was present in ancient rocks from Mars.  In summary, carbonaceous meteorites collected at the time of or shortly after impact provide the most reliable record of the solar system’s organic inventory during the early stages of its formation.  They provide the best analogue for what organic synthesis and aqueous processing may have been like on planetary surfaces prior to life’s origin.


Amino Acid Analyses of Desert Varnish from the Sonoran and Mojave deserts

 


RANDALL S. PERRY


Department of Earth and Space Sciences


University of Washington


Seattle, Washington, USA


MICHAEL H. ENGEL


School of Geology and Geophysics


University of Oklahoma


Norman, Oklahoma, USA


OLIVER BOTTA*


Scripps Institution of Oceanography


University of California at San Diego


La Jolla, California, USA


JAMES T. STALEY


Department of Microbiology and Immunology


University of Washington


Seattle, Washington, USA


There has long been a debate as to whether desert varnish deposits are microbially mediated or are deposited by inorganic processes. Several researchers have bacteria from the surface of desert varnish suggesting that bacteria are intimately associated with varnish coatings and may play a role in their formation. To test this hypothesis, we have collected scrapings of desert varnish from the Sonoran Desert in Arizona and the Mojave Desert in California and analyzed them for amino acids.  Thirteen amino acids were found in desert varnish indicating a biogenic component of these varnishes.  Two protein amino acids that were not detected in any of the varnishes are cysteine and tryptophan. Two non-protein amino acids, b-alanine and g-amino butyric acid, were found.  These are known to be formed by enzymatic decarboxylation, thereby indicating organismal activity in varnish.  Some D-enantiomers of the amino acids were also found.  In addition to small amounts of the D-enantiomer of aspartic acid, which is rapidly formed by racemization and was present in most samples, D-alanine  and D-glutamic acid were found.  These latter two amino acids are components of the peptidoglycan cell wall material of bacteria.  L-lysine was also detected, but not diaminopimelic acid.  The combination of L-lysine, D-alanine and D-glutamic acid is characteristic of the peptidoglycan from gram-positive bacteria.  Although the presence of these biomarkers does not prove that gram-positive bacteria produce the coatings, finding them is consistent with the hypothesis that they may play a role in desert varnish formation.




The importance of chemicals from the transition zone to chemical evolution



Randall S. Perry and Vera M. Kolb


Department of Earth and Space Sciences, Astrobiology Center for Early Evolution, Box 351310, University of Washington, Seattle, Washington 98195-1310 USA


Department of Chemistry, University of Wisconsin-Parkside, Kenosha, Wisconsin 53141-2000 USA


A central interest of chemical evolution is how it led to life. The current belief is that certain chemicals existed on early Earth, and that their combinations led to biologically important molecules and eventually to life itself. What is missing, however, is a consideration of chemical evolution that did not necessarily lead to life. Instead, it may have resulted in complex chemicals, which were not suitable as information molecules under certain geological conditions, or did not fulfill some other necessary aspects of biological precursors under the environmental condition in which they formed. We are interested in investigating the preservation of organic molecules from within this transition zone that bridges the primordial organic world and the biotic world. Organic molecules interact with minerals (silica), clays and oxides that might lead to their sequestration in the deposited mineral matrix. The search for chemicals on Mars should include investigating these systems without the usual dissolution of minerals prior to organic analysis. What we learn about chemicals from a transition zone on Mars, should one exist, might also shed light on the process of chemical evolution on early Earth. Rock coatings that include oxide-rich desert varnish and silica rich bottom coatings are used as a model system for the preservation of organic chemicals on contemporary Earth.




PRESERVATION OF BIOORGANIC MOLECULES IN AMORPHOUS SILICA IN NATURE



PERRY, Randall Stewart, Earth and Space Sciences, University of Washington, Mail stop 351310, Seattle, WA 98195-1310, rsp@u.washington.edu and KOLB, Vera M., Chemistry, University of Wisconsin-Parkside, 900 Wood Rd, Kenosha, WI 53141-2000


Microbial and cellular components may become incorporated into amorphous silica either by complexation with metals or entombment. For instance, polysaccharides found in bacterial cell walls contain linear polymers of sugars that may be preserved even in arid conditions when complexed with Ca, Al, Si, Fe and Mn. Silicic acid can form a variety of complexes with ions and organic molecules, including mucopolysaccharides, glycoproteins that are enriched in hydroxyl amino acids (serine and threonine), glycine, aspartic and glutamic acids. These amino acids have been found in significant quantities in rock coatings from the Mojave and Sonoran deserts. In addition, silicic acid is expected to form organic silicate complexes (Si-O-C) with hydroxyl centers from cis-1,2-diols that are fixed at ca. 0.26nm. Candidates include some sugars, unsaturated polyhydroxy compounds, catechols (1,2-diphenols), and other compounds with rigid structures and a correct “bite” that matches the O-Si-O angle and thus make stable complexes. Flexible sugar-related substances, such as polyols and sugar acids, also make Si-O-C complexes with silicic acid if they possess at least four hydroxyl groups in a particular stereochemical arrangement. From these examples it is possible to see how various organic compounds, bacteria and fungi, or their remains, can make Si-O-C complexes with silicic acid and contribute to the crosslinking and hardening of the silicate polymers. Significantly, silicic acid also makes Si-O-metal complexes, such as the Si-O-Fe complex with ferrihydrate. This means that not only organic substances, but metals as well, can participate in polymerizing, crosslinking and hardening (by elimination of water) of silicic acid. The process of formation of desert varnish, rock coatings, and silica glazes may be silicification via dissolution of silicates. Small quantities of silicic (Si(OH)4) or (di)silicic ((HO)3Si-O-Si(OH)3) acids form particles of condensed silica that fuse by gelling. Bacteria, fungi, and microcolonial fungi (arid extremophiles), might become silicified and incorporated into the coatings and glazes. The study of organic components in silica coatings may aid in understanding the process of formation of rock coatings, biomineralization, bacterial fossilization, and their past environments.




Archaeal and Bacterial Molecular Biology of Desert Varnish


 

Randall S. Perry, * Jeremy Dodsworth†, James T. Staley†



*Department of Earth and Space Sciences, Astrobiology Group, University of Washington, Seattle Washington 98195-1310



†Department of Microbiology and Immunology, School of Medicine, University of Washington, Seattle, Washington 98195-1310


 


Desert varnish is a dark coating that forms on rocks and archaeological monuments in arid and semi-arid regions throughout the world. It is composed primarily of oxygen, silicon, and aluminum, iron and manganese oxides, and, normally, lesser amounts potassium, calcium, titanium, magnesium, sodium, sulphur, phosphorous, barium, carbon, and nitrogen. Water, several polyfunctional organic compounds and amino acids have also been found. The process of formation is complex and not yet fully understood, and it has been argued that its genesis may be either biological or inorganic. The inorganic chemistry of varnish coatings has been well studied while the organic components have been less studied. The presence of labile compounds such as serine, presents a paradox that may be answered by its sequestration in or on clays or in an amorphous silicate matrix. Previous culture based studies have found primarily Gram-positive bacteria, and amino acids analyses supports the likelihood of an association with Gram-positive bacteria. However, culture-based techniques tend to underestimate microbial diversity.  We report here for the first time results of a culture-independent technique for assessing microbial  diversity on  rock  coatings. DNA was extracted from varnish coatings, and using PCR to amplify 16SrRNA, both Archaea and Bacteria rRNA were amplified. Clone libraries of bacterial- and archaeal-specific PCR product from desert varnish were constructed. Phylogenetic analyses, using full-length sequences, were done. This study indicates that there are a wide variety of prokaryotic microorganisms on or in varnish surfaces and that some primary producers may also be present.