Matching Items (42)
Description
Many acidic hot springs in Yellowstone National Park support microbial iron oxidation, reduction, or microbial iron redox cycling (MIRC), as determined by microcosm rate experiments. Microbial dissimilatory iron reduction (DIR) was detected in numerous systems with a pH < 4. Rates of DIR are influenced by the availability of ferric minerals and organic carbon. Microbial iron oxidation (MIO) was detected from pH 2 – 5.5. In systems with abundant Fe (II), dissolved oxygen controls the presence of MIO. Rates generally increase with increased Fe(II) concentrations, but rate constants are not significantly altered by additions of Fe(II). MIRC was detected in systems with abundant ferric mineral deposition.
The rates of microbial and abiological iron oxidation were determined in a variety of cold (T= 9-12°C), circumneutral (pH = 5.5-9) environments in the Swiss Alps. Rates of MIO were measured in systems up to a pH of 7.4; only abiotic processes were detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39-89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where MIO was measured. Speciation calculations reveal that ferrous iron typically exists as FeCO30, FeHCO3+, FeSO40 or Fe2+ in these systems. The presence of ferrous (bi)carbonate species appear to increase abiotic iron oxidation rates relative to locations without significant concentrations. This approach, integrating geochemistry, rates, and community composition, reveals biogeochemical conditions that permit MIO, and locations where the abiotic rate is too fast for the biotic process to compete.
For a reaction to provide habitability for microbes in a given environment, it must energy yield and this energy must dissipate slowly enough to remain bioavailable. Thermodynamic boundaries exist at conditions where reactions do not yield energy, and can be quantified by calculations of chemical energy. Likewise, kinetic boundaries exist at conditions where the abiotic reaction rate is so fast that reactants are not bioavailable; this boundary can be quantified by measurements biological and abiological rates. The first habitability maps were drawn, using iron oxidation as an example, by quantifying these boundaries in geochemical space.
The rates of microbial and abiological iron oxidation were determined in a variety of cold (T= 9-12°C), circumneutral (pH = 5.5-9) environments in the Swiss Alps. Rates of MIO were measured in systems up to a pH of 7.4; only abiotic processes were detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39-89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where MIO was measured. Speciation calculations reveal that ferrous iron typically exists as FeCO30, FeHCO3+, FeSO40 or Fe2+ in these systems. The presence of ferrous (bi)carbonate species appear to increase abiotic iron oxidation rates relative to locations without significant concentrations. This approach, integrating geochemistry, rates, and community composition, reveals biogeochemical conditions that permit MIO, and locations where the abiotic rate is too fast for the biotic process to compete.
For a reaction to provide habitability for microbes in a given environment, it must energy yield and this energy must dissipate slowly enough to remain bioavailable. Thermodynamic boundaries exist at conditions where reactions do not yield energy, and can be quantified by calculations of chemical energy. Likewise, kinetic boundaries exist at conditions where the abiotic reaction rate is so fast that reactants are not bioavailable; this boundary can be quantified by measurements biological and abiological rates. The first habitability maps were drawn, using iron oxidation as an example, by quantifying these boundaries in geochemical space.
ContributorsSt Clair, Brian (Author) / Shock, Everett L (Thesis advisor) / Anbar, Ariel (Committee member) / Garcia-Pichel, Ferran (Committee member) / Hartnett, Hilairy (Committee member) / Arizona State University (Publisher)
Created2017
Description
Biological soil crusts (biocrust) are photosynthetic communities of organisms forming in the top millimeters of unvegetated soil. Because soil crusts contribute several ecosystem services to the areas they inhabit, their loss under anthropogenic pressure has negative ecological consequences. There is a considerable interest in developing technologies for biocrust restoration such as biocrust nurseries to grow viable inoculum and the optimization of techniques for field deployment of this inoculum. For the latter, knowledge of the natural rates of biocrust dispersal is needed. Lateral dispersal can be based on self-propelled motility by component microbes, or on passive transport through propagule entrainment in runoff water or wind currents, all of which remain to be assessed. I focused my research on determining the capacity of biocrust for lateral self-propelled dispersal. Over the course of one year, I set up two greenhouse experiments where sterile soil substrates were inoculated with biocrusts and where the lateral advancement of biocrust and their cyanobacteria was monitored using time-course photography, discrete determination of soil chlorophyll a concentration, and microscopic observations. Appropriate uninoculated controls were also set up and monitored. These experiments confirm that cyanobacterial biological soil crusts are capable of laterally expanding when provided with presumably optimal watering regime similar to field conditions and moderate temperatures. The maximum temperatures of Sonoran Desert summer (up to 42 °C), exacerbated in the greenhouse setting (48 °C), caused a loss of biomass and the cessation of lateral dispersal, which resumed as temperature decreased. In 8 independent experiments, biocrust communities advanced laterally at an average rate of 2 cm per month, which is half the maximal rate possible based on the instantaneous speed of gliding motility of the cyanobacterium Microcoleus vaginatus. In a span of three months, populations of M. vaginatus, M. steenstrupii, and Scytonema spp. advanced 1 cm/month on average. The advancing crust front was found to be preferentially composed of hormogonia (differentiated, fast-gliding propagules of cyanobacteria). Having established the potential for laterally self-propelled community dispersal (without wind or runoff contributions) will help inform restoration efforts by proposing minimal inoculum size and optimal distance between inoculum patches.
ContributorsSorochkina, Kira (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Rowe, Helen (Committee member) / Wu, Jianguo (Committee member) / Arizona State University (Publisher)
Created2017
Description
Biological soil crusts (BSCs), topsoil microbial assemblages typical of arid land ecosystems, provide essential ecosystem services such as soil fertilization and stabilization against erosion. Cyanobacteria and lichens, sometimes mosses, drive BSC as primary producers, but metabolic activity is restricted to periods of hydration associated with precipitation. Climate models for the SW United States predict changes in precipitation frequency as a major outcome of global warming, even if models differ on the sign and magnitude of the change. BSC organisms are clearly well adapted to withstand desiccation and prolonged drought, but it is unknown if and how an alteration of the precipitation frequency may impact community composition, diversity, and ecosystem functions. To test this, we set up a BSC microcosm experiment with variable precipitation frequency treatments using a local, cyanobacteria-dominated, early-succession BSC maintained under controlled conditions in a greenhouse. Precipitation pulse size was kept constant but 11 different drought intervals were imposed, ranging between 416 to 3 days, during a period of 416 days. At the end of the experiments, bacterial community composition was analyzed by pyrosequencing of the 16s rRNA genes in the community, and a battery of functional assays were used to evaluate carbon and nitrogen cycling potentials. While changes in community composition were neither marked nor consistent at the Phylum level, there was a significant trend of decreased diversity with increasing precipitation frequency, and we detected particular bacterial phylotypes that responded to the frequency of precipitation in a consistent manner (either positively or negatively). A significant trend of increased respiration with increasingly long drought period was detected, but BSC could recover quickly from this effect. Gross photosynthesis, nitrification and denitrification remained essentially impervious to treatment. These results are consistent with the notion that BSC community structure adjustments sufficed to provide significant functional resilience, and allow us to predict that future alterations in precipitation frequency are unlikely to result in severe impacts to BSC biology or ecological relevance.
ContributorsMyers, Natalie Kristine (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Hall, Sharon (Committee member) / Turner, Benjamin (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2013
Description
Some cyanobacteria, referred to as boring or euendolithic, are capable of excavating tunnels into calcareous substrates, both mineral and biogenic. The erosive activity of these cyanobacteria results in the destruction of coastal limestones and dead corals, the reworking of carbonate sands, and the cementation of microbialites. They thus link the biological and mineral parts of the global carbon cycle directly. They are also relevant for marine aquaculture as pests of mollusk populations. In spite of their importance, the mechanism by which these cyanobacteria bore remains unknown. In fact, boring by phototrophs is geochemically paradoxical, in that they should promote precipitation of carbonates, not dissolution. To approach this paradox experimentally, I developed an empirical model based on a newly isolated euendolith, which I characterized physiologically, ultrastructurally and phylogenetically (Mastigocoleus testarum BC008); it bores on pure calcite in the laboratory under controlled conditions. Mechanistic hypotheses suggesting the aid of accompanying heterotrophic bacteria, or the spatial/temporal separation of photosynthesis and boring could be readily rejected. Real-time Ca2+ mapping by laser scanning confocal microscopy of boring BC008 cells showed that boring resulted in undersaturation at the boring front and supersaturation in and around boreholes. This is consistent with a process of uptake of Ca2+ from the boring front, trans-cellular mobilization, and extrusion at the distal end of the filaments (borehole entrance). Ca2+ disequilibrium could be inhibited by ceasing illumination, preventing ATP generation, and, more specifically, by blocking P-type Ca2+ ATPase transporters. This demonstrates that BC008 bores by promoting calcite dissolution locally at the boring front through Ca2+ uptake, an unprecedented capacity among living organisms. Parallel studies using mixed microbial assemblages of euendoliths boring into Caribbean, Mediterranean, North and South Pacific marine carbonates, demonstrate that the mechanism operating in BC008 is widespread, but perhaps not universal.
ContributorsRamírez-Reinat, Edgardo L (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Chandler, Douglas (Committee member) / Farmer, Jack (Committee member) / Neuer, Susanne (Committee member) / Arizona State University (Publisher)
Created2010
Description
The study of organismal adaptations oftentimes focuses on specific, constant conditions, but environmental parameters are characterized by more or less marked levels of variability, rather than constancy. This is important in environments like soils where microbial activity follows pulses of water availability driven by precipitation. Nowhere are these pulses more variable and unpredictable than in arid soils. Pulses constitute stressful conditions for bacteria because they cause direct cellular damage that must be repaired and they force cells to toggle between dormancy and active physiological states, which is energetically taxing. I hypothesize that arid soil microorganisms are adapted to the variability in wet/dry cycles itself, as determined by the frequency and duration of hydration pulses. To test this, I subjected soil microbiomes from the Chihuahuan Desert to controlled incubations for a total common growth period of 60 hours, but separated into treatments in which the total active time was reached with hydration pulses of different length with intervening periods of desiccation, so as to isolate pulse length and frequency as the varying factors in the experiment. Using 16S rRNA amplicon data, I characterized changes in microbiome growth, diversity, and species composition, and tracked the individual responses to treatment intensity in the 447 most common bacterial species (phylotypes) in the soil. Considering knowledge of extremophile microbiology, I hypothesized that growth yield and diversity would decline with shorter pulses. I found that microbial diversity was indeed a direct function of pulse length, but surprisingly, total yield was an inverse function of it. Pulse regime treatments resulted in progressively more significant differences in community composition with increasing pulse length, as differently adapted phylotypes became more prominent. In fact, more than 30% of the most common bacterial phylotypes demonstrated statistically significant population growth responses to pulse length. Most responsive phylotypes were apparently best adapted to short pulse regimes (known in the literature as Nimble Responders or NIRs), while fewer did better under long pulse regimes (known as TORs or Torpid Responders). Examples of extreme NIRs and TORs could be found among bacteria from different phyla, indicating that these adaptations have occurred multiple times during evolution.
ContributorsKut, Patrick John (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Sala, Osvaldo (Committee member) / Zhu, Qiyun (Committee member) / Arizona State University (Publisher)
Created2023
Description
The oceanic biological carbon pump is a key component of the global carbon cycle in which dissolved carbon dioxide is taken up by phytoplankton during photosynthesis, a fraction of which then sinks to depth and contributes to oceanic carbon storage. The small-celled phytoplankton (<5 µm) that dominate the phytoplankton community in oligotrophic oceans have traditionally been viewed as contributing little to export production due to their small size. However, recent studies have shown that the picocyanobacterium Synechococcus produces transparent exopolymer particles (TEP), the sticky matrix of marine aggregates, and forms abundant microaggregates (5-60 µm), which is enhanced under nutrient limited growth conditions. Whether other small phytoplankton species exude TEP and form microaggregates, and if these are enhanced under growth-limiting conditions remains to be investigated. This study aims to analyze how nutrient limitation affects TEP production and microaggregate formation of species that are found to be associated with sinking particles in the Sargasso Sea. The pico-cyanobacterium Prochlorococcus marinus (0.8 µm), the nano-diatom Minutocellus polymorphus (2 µm), and the pico-prasinophyte Ostreococcus lucimarinus (0.6 µm) were grown in axenic batch culture experiments under nutrient replete and limited conditions. It was hypothesized that phytoplankton subject to nutrient limitation will aggregate more than those under replete conditions due to an increased exudation of TEP and that Minutocellus would produce the most TEP and microaggregates while Prochlorococcus would produce the least TEP and microaggregates of the three phytoplankton groups. As hypothesized, nutrient limitation increased TEP concentration in all three species, however they were only significant in nitrogen-limited treatments of Prochlorococcus as well as nitrogen- and phosphorus-limited treatments of Minutocellus. Formation of microaggregates was significantly enhanced in Minutocellus and Ostreococcus cultures in distinct microaggregate size ranges. Minutocellus produced the most TEP per cell and aggregated at higher volume concentrations compared to Prochlorococcus and Ostreococcus. Surprisingly, Ostreococcus produced more TEP than Prochlorococcus and Minutocellus per unit cell volume. These findings show for the first time how nutrient limited conditions enhance TEP production and microaggregation of Prochlorococcus, Minutocellus, and Ostreococcus, providing a mechanism for their incorporation into larger, sinking particles and contribution to export production in oligotrophic oceans.
ContributorsShurtleff, Catrina (Author) / Neuer, Susanne (Thesis advisor) / Lomas, Michael W. (Committee member) / Garcia-Pichel, Ferran (Committee member) / Arizona State University (Publisher)
Created2022
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Improving cyanobacterial hydrogen production through bioprospecting of natural microbial communities
Description
Some cyanobacteria can generate hydrogen (H2) under certain physiological conditions and are considered potential agents for biohydrogen production. However, they also present low amounts of H2 production, a reaction reversal towards H2 consumption, and O2 sensitivity. Most attempts to improve H2 production have involved genetic or metabolic engineering approaches. I used a bio-prospecting approach instead to find novel strains that are naturally more apt for biohydrogen production. A set of 36, phylogenetically diverse strains isolated from terrestrial, freshwater and marine environments were probed for their potential to produce H2 from excess reductant. Two distinct patterns in H2 production were detected. Strains displaying Pattern 1, as previously known from Synechocystis sp. PCC 6803, produced H2 only temporarily, reverting to H2 consumption within a short time and after reaching only moderately high H2 concentrations. By contrast, Pattern 2 cyanobacteria, in the genera Lyngbya and Microcoleus, displayed high production rates, did not reverse the direction of the reaction and reached much higher steady-state H2 concentrations. L. aestuarii BL J, an isolate from marine intertidal mats, had the fastest production rates and reached the highest steady-state concentrations, 15-fold higher than that observed in Synechocystis sp. PCC 6803. Because all Pattern 2 strains originated in intertidal microbial mats that become anoxic in dark, it was hypothesized that their strong hydrogenogenic capacity may have evolved to aid in fermentation of the photosynthate. When forced to ferment, these cyanobacteria display similarly desirable characteristics of physiological H2 production. Again, L. aestuarii BL J had the fastest specific rates and attained the highest H2 concentrations during fermentation, which proceeded via a mixed-acid pathway to yield acetate, ethanol, lactate, H2, CO2 and pyruvate. The genome of L. aestuarii BL J was sequenced and bioinformatically compared to other cyanobacterial genomes to ascertain any potential genetic or structural basis for powerful H2 production. The association hcp exclusively in Pattern 2 strains suggests its possible role in increased H2 production. This study demonstrates the value of bioprospecting approaches to biotechnology, pointing to the strain L. aestuarii BL J as a source of useful genetic information or as a potential platform for biohydrogen production.
ContributorsKothari, Ankita (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Vermaas, Willem F J (Committee member) / Rittmann, Bruce (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2013
Description
There is a growing consensus that photodegradation accelerates litter decomposition in drylands, but the mechanisms are not well understood. In a previous field study examining how exposure to solar radiation affects decomposition of 12 leaf litter types over 34 months in the Sonoran Desert, litter exposed to UV/blue wavebands of solar radiation decayed faster. The concentration of water-soluble compounds was higher in decayed litter than in new (recently senesced) litter, and higher in decayed litter exposed to solar radiation than other decayed litter. Microbial respiration of litter incubated in high relative humidity for 1 day was greater in decayed litter than new litter and greatest in decayed litter exposed to solar radiation. Respiration rates were strongly correlated with decay rates and water-soluble concentrations of litter. The objective of the current study was to determine why respiration rates were higher in decayed litter and why this effect was magnified in litter exposed to solar radiation. First, I evaluated whether photodegradation enhanced the quantity of dissolved organic carbon (DOC) in litter by comparing DOC concentrations of photodegraded litter to new litter. Second, I evaluated whether photodegradation increased the quality of DOC for microbial utilization by measuring respiration of leachates with equal DOC concentrations after applying them to a soil inoculum. I hypothesized that water vapor sorption may explain differences in respiration among litter age or sunlight exposure treatments. Therefore, I assessed water vapor sorption of litter over an 8-day incubation in high relative humidity. Water vapor sorption rates over 1 and 8 days were slower in decayed than new litter and not faster in photodegraded than other decayed litter. However, I found that 49-78% of the variation in respiration could be explained by the relative amount of water litter absorbed over 1 day compared to 8 days, a measure referred to as relative water content. Decayed and photodegraded litter had higher relative water content after 1 day because it had a lower water-holding capacity. Higher respiration rates of decayed and photodegraded litter were attributed to faster microbial activation due to greater relative water content of that litter.
ContributorsBliss, Michael Scott (Author) / Day, Thomas A. (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Throop, Heather L. (Committee member) / Arizona State University (Publisher)
Created2019
Description
Desert organisms lead harsh lives owing to the extreme, often unpredictable environmental conditions they endure. Climate change will likely make their existence even harsher. Predicting the ecological consequences of future climate scenarios thus requires understanding how the biota will be affected by climatic shifts. Biological soil crusts (biocrusts) are an important ecosystem component in arid lands, one that covers large portions of the landscape, improving soil stability and fertility. Because cyanobacteria are biocrust’s preeminent primary producers, eking out an existence during short pulses of precipitation, they represent a relevant global change object of study. I assessed how climate scenarios predicted for the Southwestern United States (US) will affect biocrusts using long-term, rainfall-modifying experimental set-ups that imposed either more intense drought, a seasonally delayed monsoon season, or a shift to smaller but more frequent precipitation events. I expected drought to be detrimental, but not a delay in the monsoon season. Surprisingly, both treatments showed similar effects on cyanobacterial community composition and population size after four years. While successionally incipient biocrusts were unaffected, mature biocrusts lost biomass and diversity with treatment, especially among nitrogen-fixing cyanobacteria. In separate experiments, I assessed the effect of rainfall with modified event size and frequency after a decade of treatment. Small, frequent rainfall events surprisingly enhanced the diversity and biomass of bacteria and cyanobacteria, with clear winners and losers: nitrogen-fixing Scytonema sp. benefited, while Microcoleus vaginatus lost its dominance. As an additional finding, I could also show that water addition is not always beneficial to biocrusts, calling into question the notion that these are strictly water-limited systems.
Finally, results interpretation was severely hampered by a lack of appropriate systematic treatment for an important group of biocrust cyanobacteria, the “Microcoleus steenstrupii complex”. I characterized the complex using a polyphasic approach, leading to the formal description of a new family (Porphyrosiphonaceae) of desiccation resistant cyanobacteria that includes 11 genera, of which 5 had to be newly described. Under the new framework, the distribution and abundance of biocrust cyanobacteria with respect to environmental conditions can now be understood. This body of work contributes significantly to explain current distributional patterns of biocrust cyanobacteria and to predict their fate in the face of climate change.
Finally, results interpretation was severely hampered by a lack of appropriate systematic treatment for an important group of biocrust cyanobacteria, the “Microcoleus steenstrupii complex”. I characterized the complex using a polyphasic approach, leading to the formal description of a new family (Porphyrosiphonaceae) of desiccation resistant cyanobacteria that includes 11 genera, of which 5 had to be newly described. Under the new framework, the distribution and abundance of biocrust cyanobacteria with respect to environmental conditions can now be understood. This body of work contributes significantly to explain current distributional patterns of biocrust cyanobacteria and to predict their fate in the face of climate change.
ContributorsMoreira Camara Fernandes, Vanessa (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Rudgers, Jennifer (Committee member) / Sala, Osvaldo (Committee member) / Penton, Christopher (Committee member) / Arizona State University (Publisher)
Created2020