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Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H[subscript 2] accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH[subscript 3]-N) from 890 ± 295 to 2040 ± 30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4%) and Methanobrevibacter (11.6%), along with acetoclastic Methanosaeta (29.3%), became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta) and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species) that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.
ContributorsEsquivel Elizondo, Sofia (Author) / Parameswaran, Prathap (Author) / Delgado, Anca (Author) / Maldonado, Juan (Author) / Rittmann, Bruce (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / School of Sustainable Engineering and the Built Environment (Contributor)
Created2016-08-11
Description
We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO[subscript 3]–) and perchlorate (ClO[subscript 4]–) in contaminated groundwater. The groundwater also contained oxygen (O[subscript 2]) and sulfate (SO[2 over 4]–), which became important electron sinks that affected the NO[subscript 3]– and ClO[subscript 4]– removal rates. Using pyrosequencing, we elucidated how important phylotypes of each “primary” microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO[2 over 4]– reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the “primary” groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.
ContributorsOntiveros-Valencia, Aura (Author) / Tang, Youneng (Author) / Zhao, Heping (Author) / Friese, David (Author) / Overstreet, Ryan (Author) / Smith, Jennifer (Author) / Evans, Patrick (Author) / Rittmann, Bruce (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor)
Created2014-07-01
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
The gastrointestinal (GI) tract is home to a complex and diverse microbial ecosystem that contributes to health or disease in many aspects. While bacterial species are the majority in the GI tract, their cohabitants, fungal species, should not be forgotten. Children with autism spectrum disorder (ASD) often suffer from GI disorders and associated symptoms, implying a role the bacterial and fungal gut microbiota play in maintaining human health. The irregularities in GI symptoms can negatively affect the overall quality of life or even worsen behavioral symptoms the children present. Even with the increase in the availability of next-generation sequencing technologies, the composition and diversities of fungal microbiotas are understudied, especially in the context of ASD. We therefore aimed to investigate the gut mycobiota of 36 neurotypical children and 38 children with ASD. We obtained stool samples from all participants, as well as autism severity and GI symptom scores to help us understand the effect the mycobiome has on these symptoms. By targeting the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA V4 regions, we obtained fungal and bacterial amplicon sequences, from which we investigated the diversities, composition, and potential link between two different ecological clades. From fungal amplicon sequencing results, we observed a significant decrease in the observed fungal OTUs in children with ASD, implying a lack of potentially beneficial fungi in ASD subjects. We performed Bray-Curtis principal coordinates analysis and observed significant differences in fungal microbiota composition between the two groups. Taxonomic analysis showed higher relative abundances of Candida , Pichia, Penicillium , and Exophiala in ASD subjects, yet due to a large dispersion of data, the differences were not statistically significant. Interestingly, we observed a bimodal distribution of Candida abundances within children with ASD. Candida's relative abundance was not significantly correlated with GI scores, but children with high Candida relative abundances presented significantly higher Autism Treatment Evaluation Checklist (ATEC) scores, suggesting a role of Candida on ASD behavioral symptoms. Regarding the bacterial gut microbiota, we found marginally lower observed OTUs and significantly lower relative abundance of Prevotella in the ASD group, which was consistent with previous studies. Taken together, we demonstrated that autism is closely linked with a distinct gut mycobiota, characterized by a loss of fungal and bacterial diversity and an altered fungal and bacterial composition.
ContributorsPatel, Jigar (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Kang, Dae Wook (Committee member) / Adams, James (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The effect of an anaerobic reductive environment produced by the oxidation of zero valent iron (ZVI) on the microbial reductive dechlorination of trichloroethylene and its applicability to in-situ bioremediation processes was investigated using microcosms and soil column studies. I learned that microbial dechlorination requires a highly reductive environment, as represented by negative values for oxidation-reduction potential (ORP), which can be maintained through the addition of reducing agents such as ZVI, or to a lesser extent, the fermentation of added substrates such as lactate. Microcosm conditions represented distance from an in-situ treatment injection well and contained different types of iron species and dechlorinating bioaugmentation cultures. Diminishing efficacy of microbial reductive dechlorination along a gradient away from the injection zone was observed, characterized by increasing ORP and decreasing pH. Results also suggested that the use of particular biostimulation substrates is key to prioritizing the dechlorination reaction against competing microbial and abiotic processes by supplying electrons needed for microbial dechlorination.
ContributorsMouti, Aatikah (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Delgado, Anca (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Hydrogen is a key indicator of microbial activity in soils/sediments and groundwater because of its role as an electron donor for reducing sulfate and nitrate and carrying out other metabolic processes. The goal of this study was to quantitatively measure the total biological hydrogen demand (TBHD) of soils and sediments in anaerobic environments. We define the total biological hydrogen demand as the sum of all electron acceptors that can be used by hydrogen-oxidizing microorganisms. Three sets of anaerobic microcosms were set up with different soils/sediments, named Carolina, Garden, and ASM. The microcosms included 25g of soil/sediment and 75 mL of anaerobic medium. 10 mL of hydrogen were pulse-fed for 100 days. Hydrogen consumption and methane production were tracked using gas chromatography. Chemical analysis of each soil was performed at the beginning of the experiment to determine the concentration of electron acceptors in the soils/sediments, including nitrate, sulfate, iron and bicarbonate. An analysis of the microbial community was done at t = 0 and at the end of the 100 days to examine changes in the microbial community due to the metabolic processes occurring as hydrogen was consumed. Carolina consumed 9810 43 mol of hydrogen and produced 19,572 2075 mol of methane. Garden consumed 4006 33 mol of hydrogen and produced 7,239 543 mol of methane. Lastly, ASM consumed 1557 84 mol of hydrogen and produced 1,325 715 mol of methane. I conclude that the concentration of bicarbonate initially present in the soil had the most influence over the hydrogen demand and microbial community enrichment. To improve this research, I recommend that future studies include a chemical analysis of final soil geochemistry conditions, as this will provide with a better idea of what pathway the hydrogen is taking in each soil.
ContributorsLuna Aguero, Marisol (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Delgado, Anca (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
In the United States, the prevalence of pediatric obesity has increased to 17% in the general population and even more so in the Hispanic pediatric population to 22.4%. These children are at a higher risk for associated comorbidities, including cardiovascular disease and insulin resistance. The purpose of the following study is to determine the effectiveness of the Nutrition and Health Awareness curriculum at reducing childhood obesity by evaluating alterations in the gut microbial composition, diet, and overall health of the students throughout the five-week program. Nutrition and Health Awareness (NHA) is a student organization that strives to reduce the prevalence of obesity, diabetes, and cardiovascular diseases, specifically in children, by providing active nutrition education services through peer mentoring in elementary schools and community programs. This study went through ASU's Institutional Review Board process and all forms were translated into Spanish. The control group maintained their normal routines and the experimental group received the 5 week NHA program and then continued with their normal routines. Anthropometric measures (Body Mass Index, waist-to-hip ratio, and blood pressure), diet measures (Hispanic food frequency questionnaire), fecal swabs, and content surveys were collected on weeks 0, 5, and 8. Contrary to expected, alpha diversity, kilocalorie intake, and macronutrient intake decreased as the study progressed for both the control and experimental groups. Anthropometric measurements were relatively stable. Though not statistically significant, the greatest difference in time points is between weeks 1 and 8. This decrease in alpha diversity and kilocalorie intake could be due to a change in environment since the children started school on week 8. Future implications of this study are that parental involvement is necessary for an effective, sustainable change in these children. More research in different settings is necessary to determine NHA's effectiveness
ContributorsPatel, Kapila Cristina (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Whisner, Corrie (Committee member) / School of Nutrition and Health Promotion (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Microorganisms can produce metabolites in the gut including short chain fatty acids, vitamins, and amino acids. Certain metabolites produced in the gut can affect the brain through changes in neurotransmitter concentrations. Serotonin, a neurotransmitter, is associated with mood, appetite, and sleep. Up to 90% of serotonin synthesis is located in the gut, by human enterochromaffin cells. Bacteria known to biosynthesize tryptophan, precursor to serotonin, include Escherichia coli, Enterococcus and Streptococcus. Tryptophan is synthesized by bacteria with the enzyme tryptophan synthase and requires Vitamin B6 (Pyridoxal). We hypothesize that gut isolates from surgical weight loss patients can enhance tryptophan production, which relies on vitamin B6 availability. Our goal was to isolate bacteria in order to test for tryptophan production and to determine how Vitamin B6 concentrations could affect tryptophan production. We isolated gut bacteria was from successful surgical weight loss patient with selective pressures for Enterobacter isolates and Enterococcus isolates. We tested the isolates were tested to determine if they could biosynthesize tryptophan in-vitro. Bacterial cultures were enriched with yeast and enriched with serine and indole, substrates necessary for tryptophan biosynthesis. We analyzed the supernatant samples for tryptophan production using GC-FID. Bacterial isolates most closely related to E. coli and Klebsiella based on 16S rRNA gene sequences, produced tryptophan in vitro. While under serine & indole media conditions, R1, the isolate most similar to Klebsiella produced more tryptophan than R14, the isolate most similar to E. coli. We tested the R1 isolate with a gradient of vitamin B6 concentrations from 0.02 µg/mL to 0.2 µg/mL to determine its effect on tryptophan production. When less than 0.05 µg/mL of Vitamin B6 was added, tryptophan production at 6 hours was higher than tryptophan production with Vitamin B6 concentrations at 0.05 µg/mL and above. The production and consumption of tryptophan by Klebsiella under 0 µg/mL and 0.02 µg/mL concentrations of Vitamin B6 occurred at a faster rate when compared to concentrations 0.05 µg/mL or higher of Vitamin B6.
ContributorsYee, Emily L. (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Ilhan, Zehra (Committee member) / W. P. Carey School of Business (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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