Browsing by Author "Olson, Julie B."
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Item Aqueous geochemistry of a sulfurous freshwater spring: implications for sulfur cycling and resident microbial communities(University of Alabama Libraries, 2014) Morrissey, Tacoma Nicole; Aharon, Paul; University of Alabama TuscaloosaBlount Springs offers a sulfide-rich environment inhabited by a diverse microbial community in which to study the sulfur redox reactions and the microbially mediated processes via the analysis of sulfur isotopes of sulfide and sulfate. The average δ34SH2S at the wellheads is +31.1 ±0.3 / (n=9) and the average δ34SSO4 in the biofilm and downstream locations is highly variable with a mean value of +16.9 ±7.5 / (n=9). Sulfur isotope fractionations from H2S to SO4 range from 7.1 to 13.9 /. Utilizing the sulfur isotope fractionations it is concluded that (i) the sulfide is most likely derived from Thermochemical Sulfate Reduction (TSR) in the subsurface; (ii) the sulfide is subsequently oxidized to sulfate via the microbially related process of chemosynthetic sulfide oxidation; and (iii) the sulfide is also likely consumed by the abiotic processes of sulfide oxidation and outgassing of H2S. The isotopic fractionations from H2S to SO4 corroborate the isotopic fractionations observed in the laboratory during chemosynthetic sulfide oxidation. The carbon isotopic composition of DIC and the concentration of DIC support the hypothesis of microbial consumption of organic matter. Visualization of the biofilm via macroscopic and microscopic imaging revealed a morphologically diverse community. Biofilm of white, pink, and orange color were observed over the course of the study. Microscopic images revealed rod-shaped, coccoid, and filamentous cells. PCR amplification confirmed the presence of bacterial DNA. Aerobic lithotrophs, such as Thioplaca and Beggiatoa are possible groups of bacteria responsible for the chemosynthetic oxidation of sulfide at Blount Springs.Item Associations between Perceptions of Drinking Water Service Delivery and Measured Drinking Water Quality in Rural Alabama(MDPI, 2014) Wedgworth, Jessica C.; Brown, Joe; Johnson, Pauline; Olson, Julie B.; Elliott, Mark; Forehand, Rick; Stauber, Christine E.; University of Alabama Tuscaloosa; Georgia Institute of Technology; Georgia State UniversityAlthough small, rural water supplies may present elevated microbial risks to consumers in some settings, characterizing exposures through representative point-of-consumption sampling is logistically challenging. In order to evaluate the usefulness of consumer self-reported data in predicting measured water quality and risk factors for contamination, we compared matched consumer interview data with point-of-survey, household water quality and pressure data for 910 households served by 14 small water systems in rural Alabama. Participating households completed one survey that included detailed feedback on two key areas of water service conditions: delivery conditions (intermittent service and low water pressure) and general aesthetic characteristics (taste, odor and color), providing five condition values. Microbial water samples were taken at the point-of-use (from kitchen faucets) and as-delivered from the distribution network (from outside flame-sterilized taps, if available), where pressure was also measured. Water samples were analyzed for free and total chlorine, pH, turbidity, and presence of total coliforms and Escherichia coli. Of the 910 households surveyed, 35% of participants reported experiencing low water pressure, 15% reported intermittent service, and almost 20% reported aesthetic problems (taste, odor or color). Consumer-reported low pressure was associated with lower gauge-measured pressure at taps. While total coliforms (TC) were detected in 17% of outside tap samples and 12% of samples from kitchen faucets, no reported water service conditions or aesthetic characteristics were associated with presence of TC. We conclude that consumer-reported data were of limited utility in predicting potential microbial risks associated with small water supplies in this setting, although consumer feedback on low pressure-a risk factor for contamination-may be relatively reliable and therefore useful in future monitoring efforts.Item Associations between Self-Reported Gastrointestinal Illness and Water System Characteristics in Community Water Supplies in Rural Alabama: A Cross-Sectional Study(PLOS, 2016) Stauber, Christine E.; Wedgworth, Jessica C.; Johnson, Pauline; Olson, Julie B.; Ayers, Tracy; Elliott, Mark; Brown, Joe; Georgia State University; University of Alabama Tuscaloosa; Georgia Institute of TechnologyBackground Community water supplies in underserved areas of the United States may be associated with increased microbiological contamination and risk of gastrointestinal disease. Microbial and health risks affecting such systems have not been systematically characterized outside outbreak investigations. The objective of the study was to evaluate associations between self-reported gastrointestinal illnesses (GII) and household-level water supply characteristics. Methods We conducted a cross-sectional study of water quality, water supply characteristics, and GII in 906 households served by 14 small and medium-sized community water supplies in Alabama's underserved Black Belt region. Results We identified associations between respondent-reported water supply interruption and any symptoms of GII (adjusted odds ratio (aOR): 3.01, 95% confidence interval (CI) = 1.65-5.49), as well as low water pressure and any symptoms of GII (aOR: 4.51, 95% CI = 2.5-57.97). We also identified associations between measured water quality such as lack of total chlorine and any symptoms of GII (aOR: 5.73, 95% CI = 1.09-30.1), and detection of E. coli in water samples and increased reports of vomiting (aOR: 5.01, 95% CI = 1.62-15.52) or diarrhea (aOR: 7.75, 95% CI = 2.06-29.15). Conclusions Increased self-reported GII was associated with key water system characteristics as measured at the point of sampling in a cross-sectional study of small and medium water systems in rural Alabama in 2012 suggesting that these water supplies can contribute to endemic gastro-intestinal disease risks. Future studies should focus on further characterizing and managing microbial risks in systems facing similar challenges.Item Biomineralization of giant clam shells (tridacna gigas): implications for paleoclimate applications(University of Alabama Libraries, 2016) Gannon, Michelle E.; Perez-Huerta, Alberto; Aharon, Paul; University of Alabama TuscaloosaThe giant clam, Tridacna gigas, is an important faunal component of Indo-Pacific reef ecosystems, for which its shell is often used as an environmental archive for modern and past climates. This thesis is a study of the shell microstructure of modern specimens from Palm Island, Great Barrier Reef (GBR), Australia and Huon Peninsula, Papua-New Guinea (PNG), using a combination of petrography, scanning electron microscopy (SEM), electron backscatter diffraction (EBSD) and Raman spectroscopy, as well as a microstructural comparison of fossil T. gigas through 200 ka from PNG. Daily growth increments are recognizable in all specimens through ontogeny within the internal layer. For modern T. gigas from PNG, increments are composed of pairs of organized aragonitic needles and compact, oblong crystals, whereas modern specimens from GBR are composed of shield-like crystals. The combination of nutrient availability and rainfall are likely the most significant factors controlling shell growth and it may explain the observed differences in microstructure. The external layers are composed of a dendritic microfabric, significantly enriched in 13C compared to the internal layer, suggesting a different metabolic control on layer secretion. The internal and external layers are likely mineralized independent from each other, associated with the activity of a specific mantle organ. Furthermore, needles similar to those of modern T. gigas from PNG, are observed and the widths are measured in the set of fossil T. gigas. An exception includes two mid-Holocene-aged individuals, composed of elongated crystals, oblique to the outside of the shell. The results show that widths follows a cyclic pattern, similar to those of solar radiation variability, suggesting there is a relationship between solar activity and the width of aragonitic needles. Differences between modern and mid-Holocene T. gigas, are likely associated with fundamental environmental differences. The results of this study, pointing to locality and environmental dependence, layer specific mantle biomineralization, and co-variation between needle width and solar modulation, advance the potential of giant clam shells to assist in the reconstruction of many climate parameters that were previously limited to chemical analyses. Microstructural results are additionally applicable in engineering and medical research fields.Item Determination of ontogenetic age and paleoseasonality using shell spiral deviations and chemical proxies from fossil brachiopods(University of Alabama Libraries, 2015) Clark, Joanna Victoria; Perez-Huerta, Alberto; University of Alabama TuscaloosaBrachiopods have been extensively used in paleoclimatic and paleoecological reconstructions, but their utility would greatly increase if a method were developed to determine paleoseasonality. Currently, there is no accurate and efficient method of determining seasonal seawater temperature variations from fossil brachiopods because doing so requires knowledge of specimen ontogenetic ages, which are difficult to determine. In this study, the spiral deviation methodology for determining specimen ontogenetic ages and paleoseasonality is tested using four species of fossil brachiopods, including Laqueus rubellus, Terebratula terebratula, Pseudoatrypa sp. and Platystrophia ponderosa, which range in age from the Pleistocene to the Ordovician. Specimens were analyzed for spiral deviations using R computer code developed for brachiopod shells. These shells were then analyzed for preservation using electron backscatter diffraction and scanning electron microscopy. Finally, well-preserved fossil specimens were analyzed for oxygen isotopes and Mg/Ca ratios using a mass spectrometer and laser-ablation-inductively-coupled-mass spectrometer, respectively. Chemical analyses revealed that locations of spiral deviations on shells of L. rubellus displayed a strong direct relationship with Mg concentrations, and resulting paleotemperatures were seasonal. Conversely, specimens of T. terebratula and P. ponderosa did not show a consistently strong relationship between Mg concentrations and spiral deviations, although resulting paleotemperatures from T. terebratula agreed with those from previous studies. Overall, the results from this study indicate that the spiral deviation methodology combined with chemical proxies presents great potential for utility in past seasonal seawater temperature reconstructions in pristinely preserved, biconvex fossil brachiopods.Item Diversity, structure and convergent evolution of the global sponge microbiome(Nature Portfolio, 2016) Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Bjoerk, Johannes R.; Easson, Cole; Astudillo-Garcia, Carmen; Olson, Julie B.; Erwin, Patrick M.; Lopez-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Lopez, Jose Victor; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.; University of New South Wales Sydney; University of Adelaide; Centre National de la Recherche Scientifique (CNRS); Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Centro Mediterraneo de Investigaciones Marinas y Ambientales (CMIMA); CSIC - Instituto de Ciencias del Mar (ICM); University of Alabama Tuscaloosa; University of Auckland; University of North Carolina; University of North Carolina Wilmington; Charles Darwin University; Nova Southeastern University; Universidade do Algarve; Carl von Ossietzky Universitat Oldenburg; University of Haifa; University of Munich; University of Chicago; United States Department of Energy (DOE); Argonne National Laboratory; University of California San Diego; State University of New York (SUNY) Stony Brook; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; Australian Institute of Marine ScienceSponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.Item Employing a One Health Perspective to Investigate Naegleria Fowleri and Antibiotic Resistance(University of Alabama Libraries, 2023) Stahl, Leigha M.; Olson, Julie B.The "One Health" concept recognizes that the health of people, animals, and the environment are connected. Under this umbrella of potential intersections, I investigated the microbial ecology of Naegleria fowleri, known as the "brain eating" amoebae, and patterns of antibiotic resistance in bacteria isolated from animals at a zoo and wildlife rehabilitation center. N. fowleri thrives in freshwater and can infect humans during recreational water activities, often leading to fatal primary amoebic meningoencephalitis (PAM), emphasizing the need to understand how this amoeba persists in the environment to decrease human exposure. In my second chapter, I reviewed the abiotic and biotic factors affecting the distribution of N. fowleri within the environment. In chapter three, I studied the interactive effects of three abiotic factors (temperature, salinity, and pH) on N. fowleri growth in deionized water and environmental water. Results indicated that N. fowleri growth was highest at 25° C, and multiple interactive effects occurred between the abiotic factors. My fourth chapter investigated the habitat suitability of N. fowleri across the contiguous United States for the present-day and future using ecological niche modeling using occurrence data from three datasets. Outcomes were used to project habitat suitability up to the year 2060 for three climate change scenarios. Results suggested suitable and unsuitable habitats for N. fowleri exist across the country, where the highest suitable habitat was in the southern half of the US and habitat suitability for N. fowleri generally decreased across time and future climate change scenarios. To address antibiotic resistance, I investigated patterns of antibiotic resistance in bacteria isolated from the feces of zoo mammals (Chapter 5) and raptors admitted to a rehabilitation center (Chapter 6). Using fecal samples from raptors, antibiotic resistance of bacterial isolates was evaluated using phenotypic susceptibility screening. Results suggested antibiotic resistant phenotypes occurred in raptor fecal bacteria prior to rehabilitation and upon release. Ampicillin and tetracycline resistance were common in isolates, and trimethoprim and trimethoprim-sulfamethoxazole resistance occurred after birds were housed at the rehabilitation center. This research is a necessary step to assess antibiotic resistance in wild raptors and determine what factors contribute to antibiotic resistance.Item Environmental abiotic and biotic factors affecting the distribution and abundance of Naegleria fowleri(Oxford University Press, 2021) Stahl, Leigha M.; Olson, Julie B.; University of Alabama TuscaloosaNaegleria fowleri is a free-living protozoan that resides in soil and freshwater. Human intranasal amoebae exposure through water or potentially dust particles can culminate in primary amoebic meningoencephalitis, which generally causes death. While many questions remain regarding pathogenesis, the microbial ecology of N. fowleri is even less understood. This review outlines current knowledge of the environmental abiotic and biotic factors that affect the distribution and abundance of N. fowleri. Although the impacts of some abiotic factors remain poorly investigated or inconclusive, N. fowleri appears to have a wide pH range, low salinity tolerance and thermophilic preference. From what is known about biotic factors, the amoebae preferentially feed upon bacteria and are preyed upon by other free-living amoebae. Additional laboratory and environmental studies are needed to fill in knowledge gaps, which are crucial for surveillance and management of N. fowleri in freshwaters. As surface water temperatures increase with climate change, it is likely that this amoeba will pose a greater threat to human health, suggesting that identifying its abiotic and biotic preferences is critical to mitigating this risk.Item Exploring Individual-to Population-Level Impacts of Disease on Coral Reef Sponges: Using Spatial Analysis to Assess the Fate, Dynamics, and Transmission of Aplysina Red Band Syndrome (ARBS)(PLOS, 2013) Easson, Cole G.; Slattery, Marc; Momm, Henrique G.; Olson, Julie B.; Thacker, Robert W.; Gochfeld, Deborah J.; University of Mississippi; Middle Tennessee State University; University of Alabama Tuscaloosa; University of Alabama BirminghamBackground: Marine diseases are of increasing concern for coral reef ecosystems, but often their causes, dynamics and are unknown. The current study investigated the epidemiology of Aplysina Red Band Syndrome (ARBS), a disease affecting the Caribbean sponge Aplysina cauliformis, at both the individual and population levels. The fates of marked healthy and ARBS-infected sponges were examined over the course of a year. Population-level impacts and transmission mechanisms of ARBS were investigated by monitoring two populations of A. cauliformis over a three year period using digital photography and diver-collected data, and analyzing these data with GIS techniques of spatial analysis. In this study, three commonly used spatial statistics (Ripley's K, Getis-Ord General G, and Moran's Index) were compared to each other and with direct measurements of individual interactions using join-counts, to determine the ideal method for investigating disease dynamics and transmission mechanisms in this system. During the study period, Hurricane Irene directly impacted these populations, providing an opportunity to assess potential storm effects on A. cauliformis and ARBS. Results: Infection with ARBS caused increased loss of healthy sponge tissue over time and a higher likelihood of individual mortality. Hurricane Irene had a dramatic effect on A. cauliformis populations by greatly reducing sponge biomass on the reef, especially among diseased individuals. Spatial analysis showed that direct contact between A. cauliformis individuals was the likely transmission mechanism for ARBS within a population, evidenced by a significantly higher number of contact-joins between diseased sponges compared to random. Of the spatial statistics compared, the Moran's Index best represented true connections between diseased sponges in the survey area. This study showed that spatial analysis can be a powerful tool for investigating disease dynamics and transmission in a coral reefItem Insidious Environmental Contributors to Parkinson's Disease Pathogenesis: Antibacterial Metabolites and Mitochondria(University of Alabama Libraries, 2025) Bushman, Timothy; Ciesla, Lukasz M.Chronic exposure to mitochondrial toxins is known to play a significant role in the pathogenesis of neurodegenerative diseases. Recent research has indicated that antibacterial compounds can contribute to mitochondrial dysfunction, increasing reactive oxygen species and causing mitochondrial death. In this dissertation, two different classes of natural antibacterial compounds were explored as potential contributors to neurodegenerative disease onset and/or progression. Cyclic dipeptides are a class of environmentally abundant compounds which are consistently shown to exhibit high antibacterial activity. Their 2,5-diketopiperazine ring structure makes them resistant to degradation and enables crossing the blood-brain barrier. The potential for cyclic dipeptides to cause dopaminergic neuron death via induction of mitochondrial dysfunction has been previously proposed but not tested. In this dissertation the extraction, isolation, and bioactivity of natural cyclic dipeptides is explored. Cyclic dipeptides displayed neurodegenerative activity in Caenorhabditis elegans and indicated ability to cross the blood-brain barrier as demonstrated in an in-vitro model of the blood-brain barrier using human brain-like endothelial cells. Finally, the generation, isolation, and bioactivity of modified cyclic dipeptides is described along with the ongoing work with retinoic acid-differentiated SH-SY5Y neurons for neurodegenerative cyclic dipeptide identification. This avenue of investigation was initially inspired during the isolation of an unidentified neurodegenerative metabolite from the soil bacteria Streptomyces venezuelae. Multiple previous studies demonstrated that the filtered extract of S. venezuelae caused dopaminergic neurodegeneration in C. elegans via mitochondrial dysfunction, however the causative compounds were unknown. This dissertation details the isolation of two macrolide compounds from S. venezuelae which cause dopaminergic neuronal death in C. elegans. Additionally, a novel technique for extracting metabolites from Streptomyces biomass--accelerated solvent extraction--is explored, and its efficacy is compared to traditional actinomycete biomass extraction techniques. This dissertation provides insight into potentially insidious environmental metabolites in the context of neurodegeneration, as well as techniques for their extraction and testing.Item Phylogenetic Diversity, Host-Specificity and Community Profiling of Sponge-Associated Bacteria in the Northern Gulf of Mexico(PLOS, 2011) Erwin, Patrick M.; Olson, Julie B.; Thacker, Robert W.; University of Alabama Birmingham; University of Alabama TuscaloosaBackground: Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. Methodology/Principal Findings: We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). Conclusions/Significance: The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient environment, allowed us to differentiate resident symbionts from potentially transient or prey bacteria. Pairing replicated clone library construction with rapid community profiling via T-RFLP analyses will greatly facilitate future studies of sponge-microbe symbioses.Item The Prevalence and Distribution of Neurodegenerative Compound-Producing Soil Streptomyces spp.(Nature Portfolio, 2016) Watkins, Anna L.; Ray, Arpita; Roberts, Lindsay R.; Caldwell, Kim A.; Olson, Julie B.; University of Alabama TuscaloosaRecent work from our labs demonstrated that a metabolite(s) from the soil bacterium Streptomyces venezuelae caused dopaminergic neurodegeneration in Caenorhabditis elegans and human neuroblastoma cells. To evaluate the capacity for metabolite production by naturally occurring streptomycetes in Alabama soils, Streptomyces were isolated from soils under different land uses (agriculture, undeveloped, and urban). More isolates were obtained from agricultural than undeveloped soils; there was no significant difference in the number of isolates from urban soils. The genomic diversity of the isolates was extremely high, with only 112 of the 1509 isolates considered clones. A subset was examined for dopaminergic neurodegeneration in the previously established C. elegans model; 28.3% of the tested Streptomyces spp. caused dopaminergic neurons to degenerate. Notably, the Streptomyces spp. isolates from agricultural soils showed more individual neuron damage than isolates from undeveloped or urban soils. These results suggest a common environmental toxicant(s) within the Streptomyces genus that causes dopaminergic neurodegeneration. It could also provide a possible explanation for diseases such as Parkinson's disease (PD), which is widely accepted to have both genetic and environmental factors.Item Secondary ion mass spectrometer geochemical analysis of secondary infilled areas in stylaster erubescens;(University of Alabama Libraries, 2014) Cobb, Robin Michele; Andrus, C. Fred T.; University of Alabama TuscaloosaPaleoceanographers utilize geochemical proxies, such as oxygen isotopic ratios (δ;18;O), that are recorded in coral colonies to reconstruct past ocean conditions. Massive hermatypic corals precipitate skeletal aragonite with a δ;18;O composition that is in disequilibrium with seawater; therefore, compromising their use as a direct proxy for the δ;18;O of seawater (δ18;Oseawater). Previous studies on the family Stylasteridae, an ahermantypic coral, demonstrate that these corals precipitate aragonite in isotopic equilibrium with seawater. Stylasterid corals contain infilled pore spaces of secondary aragonite within the skeletal microstructure, presumably precipitated later in time. The δ;18;O values of these infilled areas have not been studied in detail to determine if they complicate paleoceanographic reconstructions. Stylaster erubescens; coral colonies were collected from the Charleston Bump (31.4°N, -78.8°W), in the Blake Plateau. Infilled and primary skeletal material was analyzed for δ;18;O values using secondary ion mass spectrometry (SIMS) on the micrometer scale. SIMS analysis determined that nine of the eleven infilled areas have δ;18;O values within analytical precision (±0.4 , 2σ) of the adjacent primary skeleton. The two infilled areas with differences in primary and secondary δ;18;O values outside 2σ analytical precision have δ;18;O values that are both higher and lower than the surrounding primary skeleton suggesting environmental changes between the time of initial precipitation and later infilling are the source of the variation. The primary skeleton is composed of 1.9% infilled area by area; therefore, when using conventional millimeter-scale sampling infilled areas would not produce a detectable offset in the geochemical record, in this coral species in this location. These results suggest S. erubescens; can be used as an environmental proxy data source in those regions and times where environmental change is minimal and coral contain few infilled pore spaces.Item The sponge microbiome project(Oxford University Press, 2017) Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon; Gonzalez, Antonio; Ackermann, Gail L.; Cerrano, Carlo; Astudillo-Garcia, Carmen; Easson, Cole; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Giorgos; McCormack, Grace P.; Feng, Guofang; Bell, James J.; Vicente, Jan; Bjork, Johannes R.; Montoya, Jose M.; Olson, Julie B.; Reveillaud, Julie; Steindler, Laura; Pineda, Mari-Carmen; Marra, Maria V.; Ilan, Micha; Taylor, Michael W.; Polymenakou, Paraskevi; Erwin, Patrick M.; Schupp, Peter J.; Simister, Rachel L.; Knight, Rob; Thacker, Robert W.; Costa, Rodrigo; Hill, Russell T.; Lopez-Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S.; Thomas, Torsten; University of New South Wales Sydney; University of California San Diego; Marche Polytechnic University; University of Auckland; Nova Southeastern University; Wageningen University & Research; Shanghai Jiao Tong University; Hellenic Centre for Marine Research; Ollscoil na Gaillimhe-University of Galway; Victoria University Wellington; University of Notre Dame; Centre National de la Recherche Scientifique (CNRS); Universite de Toulouse; Universite Toulouse III - Paul Sabatier; University of Alabama Tuscaloosa; INRAE; CIRAD; University of Haifa; Australian Institute of Marine Science; Tel Aviv University; University of North Carolina; University of North Carolina Wilmington; Carl von Ossietzky Universitat Oldenburg; University of British Columbia; State University of New York (SUNY) Stony Brook; Universidade de Lisboa; Instituto Superior Tecnico; University of Maryland Baltimore; University of Maryland Center for Environmental Science; Institute of Marine & Environmental Technology; King Abdullah University of Science & Technology; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; University of Kiel; University of QueenslandMarine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.Item The sponge microbiome project (vol 6, pg 1, 2017)(Oxford University Press, 2018) Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon; Gonzalez, Antonio; Ackermann, Gail L.; Cerrano, Carlo; Astudillo-Garcia, Carmen; Easson, Cole; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Giorgos; McCormack, Grace P.; Feng, Guofang; Bell, James J.; Vicente, Jan; Bjork, Johannes R.; Montoya, Jose M.; Olson, Julie B.; Reveillaud, Julie; Steindler, Laura; Pineda, Mari-Carmen; Marra, Maria V.; Ilan, Micha; Taylor, Michael W.; Polymenakou, Paraskevi; Erwin, Patrick M.; Schupp, Peter J.; Simister, Rachel L.; Knight, Rob; Thacker, Robert W.; Costa, Rodrigo; Hill, Russell T.; Lopez-Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S.; Thomas, Torsten; University of New South Wales Sydney; University of California San Diego; Marche Polytechnic University; University of Auckland; Nova Southeastern University; Wageningen University & Research; Shanghai Jiao Tong University; Hellenic Centre for Marine Research; Ollscoil na Gaillimhe-University of Galway; Victoria University Wellington; University of Notre Dame; Centre National de la Recherche Scientifique (CNRS); Universite de Toulouse; Universite Toulouse III - Paul Sabatier; University of Alabama Tuscaloosa; INRAE; CIRAD; University of Haifa; Australian Institute of Marine Science; Tel Aviv University; University of North Carolina; University of North Carolina Wilmington; Carl von Ossietzky Universitat Oldenburg; University of British Columbia; State University of New York (SUNY) Stony Brook; Universidade de Lisboa; Instituto Superior Tecnico; University of Maryland Baltimore; University of Maryland Center for Environmental Science; Institute of Marine & Environmental Technology; King Abdullah University of Science & Technology; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; University of Kiel; University of QueenslandItem Sulfur, carbon, and oxygen isotopes of coexisting sulfides and carbonates in gas and oil seeps from the Gulf of Mexico(University of Alabama Libraries, 2019) Morelli, Erica C.; Wielicki, Matthew; Aharon, Paul; University of Alabama TuscaloosaMicrobial processes consisting of bacterial sulfate reduction (BSR), bacterial disproportionation of sulfur (BDS), and BSR coupled with anaerobic oxidation of methane (BSR-AOM) occur in the Gulf of Mexico (GOM) at sites where hydrocarbon oil and gas seep through conduits to the seafloor. Thus far, no studies have measured the solid-phase sulfides from GOM seeps in-situ that provide a superior analogue to sulfides from the geologic record. This study employs in-situ sulfur isotope measurements by secondary ion mass spectrometry (SIMS) in authigenic sulfides associated with barites and carbonates, and isotope measurements of carbon and oxygen by isotope ratio mass spectrometry (IRMS) in coexisting carbonates from 5 sites (GC-140, GC-185, GC-272, MC-929, and GB-382) in the GOM. Pyrite grains (FeS₂) yield variable δ³⁴S values and are considerably more ³⁴S-depleted in seeps with dominant carbonate phase (GC-140 & GC-185: range of -50.5 to -9.0‰ CDT) compared to seeps with minor to dominant barite phase (GC-272 & MC-929: range -23.9 to 19.5 ‰ CDT; GB-382: range 5.3 to 25.9‰). Measurements of carbonate reveals variably ¹³C-depleted and ¹⁸O-enriched δ¹³C and δ¹⁸O values in all seeps (GC-140 & GC-185: -36.7 to -3.5‰ VPDB and 2.5 to 5.3‰ VPDB, respectively; GC-272 & MC-929: -38.0 to -1.2‰ VPDB and 1.6 to 2.5‰ VPDB, respectively; GB-382: -31.4 to -1.2‰ VPDB and -0.5 to 4.1‰ VPDB; respectively). The isotope data suggest a strong influence of: (i) BSR and BDS processes using crude oil and unlimited SO₄²⁻ supply near the sediment-water interface (GC-140 & GC-185); (ii) BSR using crude oil/ non-methane sublimated gas hydrate and variable availability of SO₄²⁻ at depth within the sediment column (GC-272 & MC-929; GB-382), or (iii) possible BSR-AOM using sublimated methane hydrate and SO₄²⁻ near the sulfate-methane transition zone (GC-272 and GB-382). Additionally, Fe-oxides reported in association with pyrites at GC-140, GC-185, and GC-272, could potentially influence fractionation of sulfur isotopes during microbial processes by promoting greater sulfur recycling and thus muting fractionation effects. The results of this study offer important insights on the high variability of sedimentary pyrites in cold seeps that has implications for the biogeochemical cycling of sulfur and carbon in marine environments.Item Transmission studies and the composition of prokaryotic communities associated with healthy and diseased Aplysina cauliformis sponges suggest that Aplysina Red Band Syndrome is a prokaryotic polymicrobial disease(Oxford University Press, 2021) Monti, Matteo; Giorgi, Aurora; Easson, Cole G.; Gochfeld, Deborah J.; Olson, Julie B.; University of Alabama Tuscaloosa; Middle Tennessee State University; University of MississippiAplysina cauliformis, the Caribbean purple rope sponge, is commonly affected by Aplysina Red Band Syndrome (ARBS). This transmissible disease manifests as circular lesions with red margins and results in bare spongin fibers. Leptolyngbya spp. appear to be responsible for the characteristic red coloration but transmission studies with a sponge-derived isolate failed to establish disease, leaving the etiology of ARBS unknown. To investigate the cause of ARBS, contact transmission experiments were performed between healthy and diseased sponges separated by filters with varying pore sizes. Transmission occurred when sponges were separated by filters with pore sizes >= 2.5 mu m, suggesting a prokaryotic pathogen(s) but not completely eliminating eukaryotic pathogen(s). Using 16S rRNA gene sequencing methods, 38 prokaryotic taxa were significantly enriched in diseased sponges, including Leptolyngbya, whereas seven taxa were only found in some, but not all, of the ARBS-affected sponges. These results do not implicate a single taxon, but rather a suite of taxa that changed in relative abundance with disease, suggesting a polymicrobial etiology as well as dysbiosis. As a better understanding of dysbiosis is gained, changes in the composition of associated prokaryotic communities may have increasing importance for evaluating and maintaining the health of individuals and imperiled coral reef ecosystems.