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- All Subjects: Biogeochemistry
- All Subjects: carbon cycling
- All Subjects: Climate Change
- Creators: Garcia-Pichel, Ferran
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
Biological soil crusts (BSCs) are critical components of arid and semiarid environments and provide the primary sources of bioavailable macronutrients and increase micronutrient availability to their surrounding ecosystems. BSCs are composed of a variety of microorganisms that perform a wide range of physiological processes requiring a multitude of bioessential micronutrients, such as iron, copper, and molybdenum. This work investigated the effects of BSC activity on soil solution concentrations of bioessential elements and examined the microbial production of organic chelators, called siderophores. I found that aluminum, vanadium, copper, zinc, and molybdenum were solubilized in the action of crusts, while nickel, zinc, arsenic, and zirconium were immobilized by crust activity. Potassium and manganese displayed behavior consistent with biological removal and mobilization, whereas phosphorus and iron solubility were dominated by abiotic processes. The addition of bioavailable nitrogen altered the effects of BSCs on soil element mobilization. In addition, I found that the biogeochemical activites of BSCs were limited by molybdenum, a fact that likely contributes to co-limitation by nitrogen. I confirmed the presence of siderophore producing microbes in BSCs. Siderophores are low-molecular weight organic compounds that are released by bacteria to increase element solubility and facilitate element uptake; siderophore production is likely the mechanism by which BSCs affect the patterns I observed in soil solution element concentrations. Siderophore producers were distributed across a range of bacterial groups and ecological niches within crusts, suggesting that siderophore production influences the availability of a variety of elements for use in many physiological processes. Four putative siderophore compounds were identified using electrospray ionization mass spectrometry; further attempts to characterize the compounds confirmed two true siderophores. Taken together, the results of my work provide information about micronutrient cycling within crusts that can be applied to BSC conservation and management. Fertilization with certain elements, particularly molybdenum, may prove to be a useful technique to promote BSC growth and development which would help prevent arid land degradation. Furthermore, understanding the effects of BSCs on soil element mobility could be used to develop useful biomarkers for the study of the existence and distribution of crust-like communities on ancient Earth, and perhaps other places, like Mars.
ContributorsNoonan, Kathryn Alexander (Author) / Hartnett, Hilairy (Thesis advisor) / Anbar, Ariel (Committee member) / Garcia-Pichel, Ferran (Committee member) / Shock, Everett (Committee member) / Sharp, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
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
Description
Dissolved organic matter (DOM) is an important part of aquatic foodwebs because it contains carbon, nitrogen, and other elements required by heterotrophic organisms. It has many sources that determine its molecular composition, nutrient content, and biological lability and in turn, influence whether it is retained and processed in the stream reach or exported downstream. I examined the composition of DOM from vascular wetland plants, filamentous algae, and riparian tree leaf litter in Sonoran Desert streams and its decomposition by stream microbes. I used a combination of field observations, in-situ experiments, and a manipulative laboratory incubation to test (1) how dominant primary producers influence DOM chemical composition and ecosystem metabolism at the reach scale and (2) how DOM composition and nitrogen (N) content control microbial decomposition and stream uptake of DOM. I found that differences in streamwater DOM composition between two distinct reaches of Sycamore Creek did not affect in-situ stream respiration and gross primary production rates. Stream sediment microbial respiration rates did not differ significantly when incubated in the laboratory with DOM from wetland plants, algae, and leaf litter, thus all sources were similarly labile. However, whole-stream uptake of DOM increased from leaf to algal to wetland plant leachate. Desert streams have the potential to process DOM from leaf, wetland, and algal sources, though algal and wetland DOM, due to their more labile composition, can be more readily retained and mineralized.
ContributorsKemmitt, Kathrine (Author) / Grimm, Nancy (Thesis advisor) / Hartnett, Hilairy (Committee member) / Throop, Heather (Committee member) / Arizona State University (Publisher)
Created2018
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
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
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
Cyanobacteria and algae living inside carbonate rocks (endoliths) have long been considered major contributors to bioerosion. Some bore into carbonates actively (euendoliths); others simply inhabit pre-existing pore spaces (cryptoendoliths). While naturalistic descriptions based on morphological identification have traditionally driven the field, modern microbial ecology has shown that this approach is insufficient to assess microbial diversity or make functional inferences. I examined endolithic microbiomes using 16S rRNA genes and lipid-soluble photosynthetic pigments as biomarkers, with the goal of reassessing endolith diversity by contrasting traditional and molecular approaches. This led to the unexpected finding that in all 41 littoral carbonate microbiomes investigated around Isla de Mona (Puerto Rico) and Menorca (Spain) populations of anoxygenic phototrophic bacteria (APBs) in the phyla Chloroflexi and Proteobacteria, were abundant, even sometimes dominant over cyanobacteria. This was not only novel, but it suggested that APBs may have been previously misidentified as morphologically similar cyanobacteria, and opened questions about their potential role as euendoliths. To test the euendolithic role of photosynthetic microbes, I set a time-course experiment exposing virgin non-porous carbonate substrate in situ, under the hypothesis that only euendoliths would be able to initially colonize it. This revealed that endolithic microbiomes, similar in biomass to those of mature natural communities, developed within nine months of exposure. And yet, APB populations were still marginal after this period, suggesting that they are secondary colonizers and not euendolithic. However, elucidating colonization dynamics to a sufficiently accurate level of molecular identification among cyanobacteria required the development of a curated cyanobacterial 16S rRNA gene reference database and web tool, Cydrasil. I could then detect that the pioneer euendoliths were in a novel cyanobacterial clade (named UBC), immediately followed by cyanobacteria assignable to known euendoliths. However, as bioerosion proceeded, a diverse set of likely cryptoendolithic cyanobacteria colonized the resulting pore spaces, displacing euendoliths. Endolithic colonization dynamics are thus swift but complex, and involve functionally diverse agents, only some of which are euendoliths. My work contributes a phylogenetically sound, functionally more defined understanding of the carbonate endolithic microbiome, and more specifically, Cydrasil provides a user-friendly framework to routinely move beyond morphology-based cyanobacterial systematics.
ContributorsRoush, Daniel (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Anbar, Ariel (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Cao, Huansheng (Committee member) / Arizona State University (Publisher)
Created2020