1,721,503 research outputs found
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Biological Soil Crusts Microbiomes: An Exploration and Investigation of Factors Influencing Biocrust Microbial Communities in Mojave Desert, USA
No full textBiological soil crusts (biocrusts) are major components in the dryland environment. They contain diverse microbial communities with crucial functions to dryland ecosystems. However, very little is known about these microorganisms because the biocrusts are defined by their external morphology which oftentimes neglect these unseen world. To better understand biocrusts microbial communities, extensive and integrated microbial research (external morphology and microorganisms) on biocrust is needed. Therefore, in my dissertation work I aimed to 1) summarize previous and current research, and identify knowledge gaps about biocrust microbes to provide baseline understanding about biocrust microorganisms, 2) identify key factors that influenced the biocrust microbes from three domains of life (archaea, bacteria, and fungi), and 3) to further expand our understanding about temporal/seasonal effect on these microorganisms. We employed amplicon-based metabarcoding sequencing to investigate biocrusts microbial communities. In chapter 2, our results showed that biocrusts microorganism are diverse and we are only at the beginning of biocrust microbes investigation because many microorganisms cannot be identified which could be new to science. We have modified sequencing protocols that work well with JTNP biocrusts and a baseline knowledge about biocrust microbes was established. Then, in chapter 3, we expanded our study to cover the Mojave Desert. To test our hypotheses that geography, soil depth, and crust types influenced biocrust microbial communities, 5 common biocrust types samples were collected from 4 sites across the Mojave desert. The results showed that 1) Biocrust in central Mojave were distinct from southern Mojave site, 2) biocrust surface harbored different microorganisms from subsurface soil, and 3) crust types displayed different community signatures. Moreover, microbials hubs species that connect biocrust microbes together were also identified. Lastly, chapter 4 concluded this dissertation by improving our baseline knowledge documenting how these microbial communities changes over the year and investigate how weather patterns that influenced these changes in microbial communities. We hypothesized, biocrust microbial communities were dynamic and weather including temperature, precipitation, wind speed, atmospheric pressure, humidity, and dew point influenced biocrust microbial composition. These findings not only improve our baseline understandings about biocrust microorganisms but also provide essential information for future biocrust management and conservation
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Transposable Element Dynamics in Genomes of Giant Insect - Killing Fungi of the Entomophthoraceae
No full textFungal family Entomophthoraceae that are obligate pathogens of insects have massive genomes, some exceeding 1 Gb. They are largely expanded by transposable elements (TEs), but the reason and impact of TE driven genome expansion remains poorly understood. This study investigates TE - mediated genome expansion, active TE families, and the mechanisms of TE silencing in these early diverging fungi. I used Extensive de-novo TE Annotator (EDTA) for de novo TE discovery and characterization in this study. I identified LTR/Ty3 retrotransposons as the primary contributors to genome expansion, with the largest TE families proliferating after species diversification. While Entomophthora muscae exhibits a compartmentalized genome distinct from the classic "two-speed genome" model, no evidence of a RIP-like mutation system for TE silencing was detected for Entomophthoraceae genomes. Notably, two active MITE families and their associated autonomous elements were identified in Entomophaga maimaiga, with insertion preferences near genes consistent with other MITE families. This study provides critical insights into TE-driven genome expansion in Entomophthoraceae, advances our understanding of their evolutionary history, and establishes a framework for characterizing active TEs in early diverging fungi
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An ‘Omics Investigation into the Effects of Aluminum Toxicity on Arabidopsis Thaliana
No full textAluminum (Al) toxicity is a global problem that leads to stoppage of root growth, overall smaller plant size and lower crop yields. Previous research has shown the molecular response of plants to Al toxicity occurs through a DNA damage response pathway involving ATR and SOG1 genes. To explore this phenomenon further both transcriptomic and genomic experiments were performed using Arabidopsis Thaliana. The goal of the transcriptomics was to determine a gene or suite of genes that were deferentially expressed with Al3+ exposure that could potentially confer Al tolerance to crop plants. While a companion genomics study aimed to understand what type of genomic damage was occurring following Al exposure. Arabidopsis seedlings were grown on gel soaked media plates in the absences or presence of Al3+, before nucleic acids were harvested for Illumina short read sequencing. Transcriptionally, a suite of genes that included known Al response factors and some novel genes were identified using a cut off of 2 fold change and a false discover rate of 1%, 10 of the genes had their expression validated using quantitative real time PCR. In addition, it was identified genetically that Al toxicity leads to the generation of one and two base pair insertions and deletions, which were determined to be statistically significant. With this knowledge future experiments can be performed with the promise of finding the molecular critical to responding to Al exposure and how to use this response to confer Al tolerance to crop plants. Such experiments should include testing Arabidopsis mutants that have reactive oxygen species related genes knocked out or overexpressed to evaluate the level of genomic damage in the presence Al3+. Additionally, genes identified from this transcriptional study should have their expression modified to further understand their role in Al toxicity. Pathway interaction studies with these factors could highlight the full molecular pathway of the plants response to Al exposure
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A Study of Comparative Analysis of Transposable Elements in filamentous fungi
No full textTransposable elements (TE) are genetic elements, which can move within the genome. TE are widely distributed in almost all organisms, both prokaryotes and eukrayotes Nearly 45% of human genomes are constituted of transposable elements. There are two major classes of transposable elements: class I and class II. Class I elements, also called retrotransposons, use a so-called "copy and paste" mechanism to replicate them and insert into new positions via an RNA intermediate. Class II elements, also called DNA transposons, don't use an RNA intermediate but a "cut and paste" mechanism to move within genomes. In some filamentous fungi, there is a genome defense mechanism called Repeat-induced Point mutation (RIP) which causes C:G to T:A mutations to transposons regions and thus repress their transposition. My research involved characterization and annotation of transposable elements in seven filamentous fungi and RIP analysis in these species. I've developed an integrated pipeline for TE identification and annotation and found evidence of RIP using the RIP indices in 5 filamentous ascomycete fungi (Neurospora crassa, Neurospora tetrasperma, Neurospora discreta, Sporotrichum thermophile, and Thielavia terrestris), but no evidence of RIP in Chaetomium globosum and Sordaria macrosporus. I found that Gyspy and Copia LTRs were the most abundant TEs. My results presented two paradoxes: 1) S.macrospora and C.globosum have low percentage of interspersed repeats but lack evidence for RIP; 2) S.thermophile and T.terrestris show evidence for RIP but also have many repeats. Moreover, I've discovered several factors related to RIP mechanism, such as the length of transposons, the type of transposons, etc
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Draft Genome Sequence of “Candidatus Spirobacillus cienkowskii,” a Pathogen of Freshwater Daphnia Species, Reconstructed from Hemolymph Metagenomic Reads
No full textWe report here the near-complete genome sequence of "Candidatus Spirobacillus cienkowskii," a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen
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Micro-Colonial Fungi Across Different Microcosms: Observing Micro-Colonial Fungi in Their Niches
No full textMicro-colonial fungi (MCF) are an extremotolerant group of polyphyletic fungi found in different extremes of this planet, from Southern Californian deserts to Antarctic tundras, and even in the lungs of cystic fibrosis patients. MCF are found in the Eurotiomycetes and Dothideomycetes classes, two lineages that diverged millions of years ago, yet MCF from both these clades have developed nearly identical features. The work described in this thesis encompasses a wide range of MCF, uncovering their unusual niches, and understanding their genomic structure. The first chapter describes three new species of MCF isolated from biological soil crusts collected from the deserts of southern California. Two MCF, respectfully, use traditional Cahuilla tribal terms for nomenclature. We introduce to you Neophaeococcomyces mojaviensis, Coniosporium tulheliwenetii, and Taxawa tesnikishii. The second chapter has us travel to Antarctica where 25 strains of an endemic MCF, Friedmanniomyces endolithicus, were collected for 40 years and analyzed for geologic spatial placement, ploidy, and mating types. Within our population of 25, we received an interesting mix of ploidies and it may be the way F. endolithicus survives the extremes of Antarctica. We were also able to place the time of F. endolithicus divergence from other Dothideomycetes to 48 million years ago, near to the time predicted when Antarctica split from Pangea and drifted to the region it is found in today. Our final chapter takes us into the lungs of a cystic fibrosis patient to find a slow-growing MCF, Exophiala dermatitidis, persisting for over three years. Twenty-four specimens of E. dermatitidis were isolated from this patient in the span of three years with countless antibiotics to clear other persistent infections. Population structure showed three different groups with varying mutational rates, phenotypic filamentation, and chromosomal structures as possible main culprits for persistence. Heterogenous phenotypes were observed in the three groups, and we could not make ties to melanin pigmentation and itraconazole antifungal therapy. Through this work, it has become increasingly clear there needs to be more effort, whether in the clinical cases or environmental, to consider the slow-growing MCFs as possible causative agents or pivotal functional characters in different extreme habitats
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Discovery and Properties of Small RNAs from Meiotic Silencing by Unpaired DNA in Neurospora crassa
No full textGenome defense likely evolved to prevent the spread of transposable elements and invading viruses. Effective genome defense mechanisms have limited colonization of the Neurospora crassa genome by transposable elements. A novel DNA transposon named Sly1-1 was discovered in the genome of the most widely used lab "wildtype" strain FGSC 2489 (OR74A). Meiotic silencing by unpaired DNA (MSUD), also simply called "meiotic silencing", prevents the expression of regions of the genome that are unpaired during karyogamy. This mechanism is posttranscriptional and involves the production of small RNA, so called "masiRNAs" by proteins homologous to those involved in RNAi silencing pathways in animals, fungi and plants. Here, I demonstrate production of small RNAs when Sly1-1 was unpaired in a cross between two wild type strains. These small RNAs are dependent on SAD-1, an RNA-dependent RNA polymerase necessary for meiotic silencing. I present the first case of endogenously produced masiRNA from a novel N. crassa DNA transposable element during the sexual development. By comparing genome sequences of two mating partners, I also identified (1) unpaired regions undergoing meiotic silencing, some of which contained the repetitive sequences and transposon relics. Small RNA produced from such regions shared the same features as masiRNAs; (2) unpaired regions immune to meiotic silencing with genes contained protected from meiotic silencing via abolishing small RNA production; (3) common regions shared by two mating patterns but with small RNAs production during karyogamy. The dissection of these regions revealed the role of meiotic silencing on resisting repetitive sequences and on compromising the unpaired genes essential in sexual development
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Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates
No full textScreening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals
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The Environment and Landscape Structure the Photobionts, the Mycobiota, and the Mycobiont of the Lichen Acarospora socialis Across Environmental Gradients in California
No full textLichens are a diverse and successful group of symbiotic organisms with nearly 20,000 species to date that occur across the world in terrestrial ecosystems from the poles to the tropics. Lichens are commonly thought of as a union between the primary fungus (mycobiont) and primary photobiont (algae and/or cyanobacteria); however, there are a plethora of other organisms that associate with the lichen symbiosis. In this dissertation I focused on the photobionts, mycobiota, and mycobiont of the lichen, Acarospora socialis, which is an areolate to squamulose lichen that is common in the Sonoran Desert region and in California. In chapter 2, I used Illumina metabarcoding to survey the photobionts of A. socialis in Joshua Tree National Park (JTNP) and found seventeen species of Trebouxia algae associating with A. socialis throughout an environmental gradient in the park. In addition, variation partitioning analysis revealed that geographic space contributed more (21%) to the variation in Trebouxia when compared to the environment (10%). These results suggest that the Trebouxia algae are dispersal limited. In addition, we also used Illumina metabarcoding of the mycobiota of A. socialis via the ITS1 marker and found three fungal phyla associated with A. socialis, with more of a contribution from Ascomycota and with some contribution from Basidiomycota and a minor composition from Chytridiomycota. In addition, the black yeast Knufia was consistently found in high abundance in the lichen mycobiota of A. socialis, with higher abundance in the higher elevations in JTNP. Finally, in chapter 4 we used whole genome Illumina resequencing and found five distinct subpopulations of the A. socialis mycobiont across the landscape of California with mycobiont diversity structured due to phylogeography, isolation by distance (IBD), and isolation by environment (IBE), although IBE was greater contributor than IBD. In addition, patterns of genetic diversity showed that coastal Southern California isolates were more diverse than the isolates from the Mojave Desert, while inland Northern California isolates of A. socialis were more diverse than coastal Northern California isolates
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Volatiles Produced by Serratia marcescens and Their Inhibitory Effects on Rhizopus stolonifer and Neurospora crassa
No full textBacteria and fungi have shared similar niches for millions and possibly billions of years. Researchers often study the antagonism between microbes to produce novel, effective antimicrobials, but often stop short of the large compounds secreted into the nearby environment. Here I show that bacteria produce antifungals that can volatilize and can inhibit fungal growth from a distance. These are even produced high enough levels to inhibit some of the fastest-growing fungi like Neurospora and Rhizopus. Further, I explore how the fungi sense, react, and protect themselves from bacteria in their vicinity through their transcriptional response to pure volatiles. This important contribution to the growing field of bacterial-fungal interactions highlights the importance of volatiles for long-distance interactions between microbes
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