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Future robotic and human missions to the Moon and Mars will need in situ capabilities to characterize the mineralogy of rocks and soils within a microtextural context. Such spatially-correlated information is considered crucial for correct petrogenetic interpretations and will be key observations for assessing the potential for past habitability on Mars. These data will also enable the selection of the highest value samples for further analysis and potential caching for return to Earth. The Multispectral Microscopic Imager (MMI), similar to a geologist's hand lens, advances the capabilities of current microimagers by providing multispectral, microscale reflectance images of geological samples, where each image pixel is comprised of a 21-band spectrum ranging from 463 to 1735 nm. To better understand the capabilities of the MMI in future surface missions to the Moon and Mars, geological samples comprising a range of Mars-relevant analog environments as well as 18 lunar rocks and four soils, from the Apollo collection were analyzed with the MMI. Results indicate that the MMI images resolve the fine-scale microtextural features of samples, and provide important information to help constrain mineral composition. Spectral end-member mapping revealed the distribution of Fe-bearing minerals (silicates and oxides), along with the presence of hydrated minerals. In the case of the lunar samples, the MMI observations also revealed the presence of opaques, glasses, and in some cases, the effects of space weathering in samples. MMI-based petrogenetic interpretations compare favorably with laboratory observations (including VNIR spectroscopy, XRD, and thin section petrography) and previously published analyses in the literature (for the lunar samples). The MMI was also deployed as part of the 2010 ILSO-ISRU field test on the slopes of Mauna Kea, Hawaii and inside the GeoLab as part of the 2011 Desert RATS field test at the Black Point Lava Flow in northern Arizona to better assess the performance of the MMI under realistic field conditions (including daylight illumination) and mission constraints to support human exploration. The MMI successfully imaged rocks and soils in outcrops and samples under field conditions and mission operation scenarios, revealing the value of the MMI to support future rover and astronaut exploration of planetary surfaces.
ContributorsNúñez Sánchez, Jorge Iván (Author) / Farmer, Jack D. (Thesis advisor) / Christensen, Philip R. (Committee member) / Garcia-Pichel, Ferran (Committee member) / Robinson, Mark S. (Committee member) / Sellar, R. Glenn (Committee member) / Williams, Lynda B. (Committee member) / Arizona State University (Publisher)
Created2012
Description
Biological soil crusts (biocrusts) are topsoil communities of organisms that contribute to soil fertility and erosion resistance in drylands. Anthropogenic disturbances can quickly damage these communities and their natural recovery can take decades. With the development of accelerated restoration strategies in mind, I studied physiological mechanisms controlling the establishment of cyanobacteria in biocrusts, since these photoautotrophs are not just the biocrust pioneer organisms, but also largely responsible for improving key soil attributes such as physical stability, nutrient content, water retention and albedo. I started by determining the cyanobacterial community composition of a variety of biocrust types from deserts in the Southwestern US. I then isolated a large number of cyanobacterial strains from these locations, pedigreed them based on their 16SrRNA gene sequences, and selective representatives that matched the most abundant cyanobacterial field populations. I then developed methodologies for large-scale growth of the selected isolates to produce location-specific and genetically autochthonous inoculum for restoration. I also developed and tested viable methodologies to physiologically harden this inoculum and improve its survival under harsh field conditions. My tests proved that in most cases good viability of the inoculum could be attained under field-like conditions. In parallel, I used molecular ecology approaches to show that the biocrust pioneer, Microcoleus vaginatus, shapes its surrounding heterotrophic microbiome, enriching for a compositionally-differentiated “cyanosphere” that concentrates the nitrogen-fixing function. I proposed that a mutualism based on carbon for nitrogen exchange between M. vaginatus and its cyanosphere creates a consortium that constitutes the true pioneer community enabling the colonization of nitrogen-poor, bare soils. Using the right mixture of photosynthetic and diazotrophic cultures will thus likely help in soil restoration. Additionally, using physiological assays and molecular meta-analyses, I demonstrated that the largest contributors to N2-fixation in late successional biocrusts (three genera of heterocystous cyanobacteria) partition their niche along temperature gradients, and that this can explain their geographic patterns of dominance within biocrusts worldwide. This finding can improve restoration strategies by incorporating climate-matched physiological types in inoculum formulations. In all, this dissertation resulted in the establishment of a comprehensive "cyanobacterial biocrust nursery", that includes a culture collection containing 101 strains, isolation and cultivation methods, inoculum design strategies as well as field conditioning protocols. It constitutes a new interdisciplinary application of microbiology in restoration ecology.
ContributorsGiraldo Silva, Ana Maria (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Barger, Nichole N (Committee member) / Bowker, Mathew A (Committee member) / Sala, Osvaldo (Committee member) / Arizona State University (Publisher)
Created2019
Description
The ability to find evidence of life on early Earth and other planets is constrained by the current understanding of biosignatures and our ability to differentiate fossils from abiotic mimics. When organisms transition from the living realm to the fossil record, their morphological and chemical characteristics are modified, usually resulting in the loss of information. These modifications can happen during early and late diagenesis and differ depending on local geochemical properties. These post-depositional modifications need to be understood to better interpret the fossil record. Siliceous hot spring deposits (sinters) are of particular interest for biosignature research as they are early Earth analog environments and targets for investigating the presence of fossil life on Mars. As silica-supersaturated fluids flow from the vent to the distal apron, they precipitate non-crystalline opal-A that fossilizes microbial communities at a range in scales (μm-cm). Therefore, many studies have documented the ties between the active microbial communities and the morphological and chemical biosignatures in hot springs. However, far less attention has been placed on understanding preservation in systems with complex mineralogy or how post-depositional alteration affects the retention of biosignatures. Without this context, it can be challenging to recognize biosignatures in ancient rocks. This dissertation research aims to refine our current understanding of biosignature preservation and retention in sinters. Biosignatures of interest include organic matter, microfossils, and biofabrics. The complex nature of hot springs requires a comprehensive understanding of biosignature preservation that is representative of variable chemistries and post-depositional alterations. For this reason, this dissertation research chapters are field site-based. Chapter 2 investigates biosignature preservation in an unusual spring with mixed opal-A-calcite mineralogy at Lýsuhóll, Iceland. Chapter 3 tracks how silica diagenesis modifies microfossil morphology and associated organic matter at Puchuldiza, Chile. Chapter 4 studies the effects of acid fumarolic overprinting on biosignatures in Gunnuhver, Iceland. To accomplish this, traditional geologic methods (mapping, petrography, X-ray diffraction, bulk elemental analyses) were combined with high-spatial-resolution elemental mapping to better understand diagenetic effects in these systems. Preservation models were developed to predict the types and styles of biosignatures that can be present depending on the depositional and geochemical context. Recommendations are also made for the types of deposits that are most likely to preserve biosignatures.
ContributorsJuarez Rivera, Marisol (Author) / Farmer, Jack D (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Shock, Everett (Committee member) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2021
Description
The experiments conducted in this report supported previous evidence (Bethany et al., 2019) that a newly identified predatory bacterium causes a higher rate of mortality in the biological soil crust cyanobacterium M. vaginatus when in hot soils than in cold soils. I predicted that the extracellular propagules of this predatory bacterium were inactivated at seasonally low temperatures, rendering them non-viable when introduced to M. vaginatus at room temperature. However, I found that the predatory bacterium became only transiently inactive at low temperatures, recovering its pathogenicity when later exposed to warmer temperatures. By contrast, inactivation of infectivity was complete by exposure in both liquid and dry conditions for five days at 40 °C. I also expected that its infectivity towards M. vaginatus was temperature dependent. Indeed, infection was hampered and did not cause high mortality when predator and prey were incubated at or below 10 °C, which could have been due to slowed metabolisms of M. vaginatus or to an inability of the predatory bacterium to attack in cold conditions. Above 10 °C, when M. vaginatus grew faster, time to full death of predator/prey incubations correlated with the rate of growth of healthy cultures.
The experiments in this study observed a correlation between the growth rate of uninfected cultures and the decay rate of infected cultures, meaning that temperatures that cultures that displayed a higher growth rate for uninfected M. vaginatus would die faster when infected with the predatory bacterium. Infected cultures that were incubated at temperatures 4 and 10 °C did not display death and this could have been due to lower activity of M. vaginatus at lower temperatures or the inability for the predatory bacterium to attack at lower temperatures.
The experiments in this study observed a correlation between the growth rate of uninfected cultures and the decay rate of infected cultures, meaning that temperatures that cultures that displayed a higher growth rate for uninfected M. vaginatus would die faster when infected with the predatory bacterium. Infected cultures that were incubated at temperatures 4 and 10 °C did not display death and this could have been due to lower activity of M. vaginatus at lower temperatures or the inability for the predatory bacterium to attack at lower temperatures.
ContributorsAhamed, Anisa Nour (Author) / Garcia-Pichel, Ferran (Thesis director) / Giraldo Silva, Ana Maria (Committee member) / Bethany Rakes, Julie (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
With the development and successful landing of the NASA Perseverance rover, there has been growing interest in identifying how evidence of ancient life may be preserved and recognized in the geologic record. Environments that enable fossilization of biological remains are termed, “taphonomic windows”, wherein signatures of past life may be detected. In this dissertation, I have sought to identify taphonomic windows in planetary-analog environments with an eye towards the exploration of Mars. In the first chapter, I describe how evidence of past microbial life may be preserved within serpentinizing systems. Owing to energetic rock-water reactions, these systems are known to host lithotrophic and organotrophic microbial communities. By investigating drill cores from the Samail Ophiolite in Oman, I report morphological and associated chemical biosignatures preserved in these systems as a result of subsurface carbonation. As serpentinites are known to occur on Mars and potentially other planetary bodies, these deposits potentially represent high-priority targets in the exploration for past microbial life. Next, I investigated samples from Atacama Desert, Chile, to understand how evidence of life may be preserved in ancient sediments formed originally in evaporative playa lakes. Here, I describe organic geochemical and morphological evidence of life preserved within sulfate-dominated evaporite rocks from the Jurassic-Cretaceous Tonel Formation and Oligocene San Pedro Formation. Because evaporative lakes are considered to have been potentially widespread on Mars, these deposits may represent additional key targets to search for evidence of past life. In the final chapter, I describe the fossilization potential of surficial carbonates by investigating Crystal Geyser, an active cold spring environment. Here, carbonate minerals precipitate rapidly in the presence of photosynthetic microbial mat communities. I describe how potential biosignatures are initially captured by mineralization, including cell-like structures and microdigitate stromatolites. However, these morphological signatures quickly degrade owing to diagenetic dissolution and recrystallization reactions, as well as textural coarsening that homogenizes the carbonate fabric. Overall, my dissertation underscores the complexity of microbial fossilization and highlights chemically-precipitating environments that may serve as high-priority targets for astrobiological exploration.
ContributorsZaloumis, Jonathan (Author) / Farmer, Jack D (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Ruff, Steven W (Committee member) / Shock, Everett L (Committee member) / Arizona State University (Publisher)
Created2021
Description
Predatory bacteria are a guild of heterotrophs that feed directly on other living bacteria. They belong to several bacterial lineages that evolved this mode of life independently and occur in many microbiomes and environments. Current knowledge of predatory bacteria is based on culture studies and simple detection in natural systems. The ecological consequences of their activity, unlike those of other populational loss factors like viral infection or grazing by protists, are yet to be assessed. During large-scale cultivation of biological soil crusts intended for arid soil rehabilitation, episodes of catastrophic failure were observed in cyanobacterial growth that could be ascribed to the action of an unknown predatory bacterium using bioassays. This predatory bacterium was also present in natural biocrust communities, where it formed clearings (plaques) up to 9 cm in diameter that were visible to the naked eye. Enrichment cultivation and purification by cell-sorting were used to obtain co-cultures of the predator with its cyanobacterial prey, as well as to identify and characterize it genomically, physiologically and ultrastructurally. A Bacteroidetes bacterium, unrelated to any known isolate at the family level, it is endobiotic, non-motile, obligately predatory, displays a complex life cycle and very unusual ultrastructure. Extracellular propagules are small (0.8-1.0 µm) Gram-negative cocci with internal two-membrane-bound compartmentalization. These gain entry to the prey likely using a suite of hydrolytic enzymes, localizing to the cyanobacterial cytoplasm, where growth begins into non-compartmentalized pseudofilaments that undergo secretion of vesicles and simultaneous multiple division to yield new propagules. I formally describe it as Candidatus Cyanoraptor togatus, hereafter Cyanoraptor. Its prey range is restricted to biocrust-forming, filamentous, non-heterocystous, gliding, bundle-making cyanobacteria. Molecular meta-analyses showed its worldwide distribution in biocrusts. Biogeochemical analyses of Cyanoraptor plaques revealed that it causes a complete loss of primary productivity, and significant decreases in other biocrusts properties such as water-retention and dust-trapping capacity. Extensive field surveys in the US Southwest revealed its ubiquity and its dispersal-limited, aggregated spatial distribution and incidence. Overall, its activity reduces biocrust productivity by 10% at the ecosystem scale. My research points to predatory bacteria as a significant, but overlooked, ecological force in shaping soil microbiomes.
ContributorsBethany Rakes, Julie Ann (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Gile, Gillian (Committee member) / Cao, Huansheng (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2022
Description
Biocrusts are microbial communities that inhabit arid soil surfaces, providing essential services to dryland ecosystems. A paradoxical filamentous cyanobacterium, Microcoleus vaginatus, resides within the biocrust. While is often pioneers the colonization of bare, nutrient-poor desert soils worldwide, it cannot fix dinitrogen. In nature, M. vaginatus coexists with a unique microbial community, a “cyanosphere”, that is characterized by a high abundance of diazotrophic heterotrophs. This suggests mutualistic relationships wherein nutrients are traded between phototrophs and heterotrophs. To explore these relationships, I performed targeted, pedigreed isolation of cyanosphere members and used co-cultivation to recreate the mutualism in culture. Results showed that, in the absence of fixed nitrogen, M. vaginatus grew well when co-cultured with cyanosphere diazotrophs, but only poorly or not at all when alone or with non-cyanosphere diazotrophs. In agreement with this, the experimental provision of nitrogen to natural populations resulted in a loss of diazotrophs from the cyanosphere compared to controls, but the addition of phosphorus did not. Additionally, the convergence of M. vaginatus trichomes into large bundles held by a common sheath was elicited in culture by the addition of cyanosphere diazotrophs, pointing to a role of cyanobacterial motility responses in the development of mutualistic interactions. I then demonstrated that the tendency of M. vaginatus to stay within bundles and close to the sheath-dwelling cyanosphere was dependent on the cyanosphere population size. This effect was likely mediated by glutamate that acted as a signaling molecule rather than as a N source and impacted the gliding speed and negative chemophobic responses on the cyanobacterium. Glutamate seems to be used as a cue to spatially optimize cyanobacterium-cyanosphere mutualistic exchanges. My findings have potential practical applications in restoration ecology, which I further pursued experimentally. Co-inoculation of soil with cyanosphere diazotrophs resulted in swifter development of biocrusts over inoculation with the cyanobacterium only. Further, their addition to disturbed native soils containing traces of cyanobacteria sufficed for the formation of cohesive biocrusts without cyanobacterial inoculation. The inclusion of such “biocrust probiotics” in biocrust restoration is recommended. Overall, this body of work elucidates the hitherto unknown role of beneficial heterotrophic bacteria in the initial formation and development of biocrusts.
ContributorsNelson, Corey (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Penton, C. Ryan (Committee member) / Gile, Gillian (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2021