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Unveiling soil microbial communities and resistomes in northern Alaska National Wildlife Refuges
Full text linkThesis (M.S.) University of Alaska Fairbanks, 2024Microbial communities residing in pristine high-latitude soils play a critical role in ecosystem function, but also harbor potential threats such as acting as reservoirs of antimicrobial resistance (AMR) genes. Current knowledge about these microbial communities and the resistance genes they carry presents limits to the ability to predict how these ecosystems will respond to climate change. This knowledge gap is particularly concerning in light of the potential public health threat posed by antimicrobial resistance harbored within these communities as antibiotic-resistant human infections continue to increase. This study investigated the microbial communities and details the antimicrobial resistance gene reservoirs in previously unsurveyed soils of three northern Alaska National Wildlife Refuges representing three distinct high-latitude biomes. I used a combination of 16S rRNA gene sequencing and metagenomic sequencing to characterize microbial community diversity and composition, as well as the AMR gene resistome. Also, I analyzed soil chemical components to evaluate their potential role in shaping these communities. My findings reveal significant geographic structure in microbial communities likely driven by differences in soil properties and dispersal limitation. Additionally, I found variation in pH significantly explained differences in alpha diversity, with slightly acidic soils harboring the highest diversity. The pattern of resistome structure matched the pattern of community structure, with microbial communities within the same refuge showing less variation than communities between refuges. Additionally, the data revealed significantly fewer AMR genes in the Selawik National Wildlife Refuge than in the other refuges. I found that variation in pH and in phosphorus concentrations significantly explained variation in AMR gene abundance with higher pH and higher phosphorus resulting in more AMR genes detected. My analysis identified that over 60% of AMR genes encoded resistance to lastresort glycopeptide antibiotics. My findings reveal that soil chemistry, particularly pH, plays a key role in shaping both microbial communities and AMR gene reservoirs in these pristine high-latitude soils. This study's characterization provides a crucial foundation for understanding how climate change and human activities might impact these ecosystems. Understanding the presence and distribution of AMR genes within microbial communities of pristine soils is essential for conserving these ecosystems and mitigating public health risks, including those associated with the spread of antibiotic resistance genes, especially those encoding resistance to last-resort antibiotics.Alaska INBRE Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103395, Biomedical Learning and Staff Training (BLaST) program at the University of Alaska Fairbanks funded through the linked awards RL5GM118990, TL4GM118992, and 1UL1GM118991Chapter One: General introduction -- 1.1 References. Chapter Two: Differentiation in soil bacterial communities of Alaska National Wildlife Refuges: a link to soil chemistry and environmental gradients -- 2.1 Abstract -- 2.2 Introduction -- 2.2.1 Study refuge description -- 2.3 Material and methods -- 2.3.1 Soil sampling -- 2.3.2 Soil chemical component analysis -- 2.3.3 165 rRNA gene sequencing and analysis -- 2.3.4 Statistical analysis -- 2.4 Results -- 2.4.1 Soil chemical component differences between refuges -- 2.4.2 Diversity pattern, composition, and environmental associations of microbial communities -- 2.4.3 Microbial dark matter -- 2.4.4 Alpha diversity differs by refuge -- 2.4.5 Significant differences in microbial community composition between refuges -- 2.4.6 Bacterial community composition -- 2.4.7 pH explains variation in alpha diversity -- 2.5 Discussion -- 2.5.1 Effective taxonomic assignment in understudied environment -- 2.5.2 Interplay between alpha diversity measures and soil pH -- 2.5.3 Beta diversity patterns and environmental convergence in two high-latitude refuges -- 2.5.4 Unveiling core taxa and refuge-specific enrichment patterns -- 2.5.5 Influence of soil chemistry on microbial community diversity -- 2.5.6 Limitations -- 2.6 Conclusion -- 2.7 Funding & acknowledgements -- 2.8 References. Chapter Three: Antibiotic resistomes reflect underlying similarities and environmental gradients in northern Alaska soils -- 3.1 Abstract -- 3.2 Introduction -- 3.3 Methods -- 3.3.1 Soil sampling -- 3.3.2 Metagenomic squencing -- 3.3.3 Metagenomic analyses -- 3.3.4 Soil chemistry -- 3.3.5 Statistical analysis -- 3.4 Results -- 3.4.1 Antibiotic resistance profile across refuges -- 3.4.2 AMR gene abundance and diversity -- 3.4.3 Beta diversity analysis rebeals variation in resistomes by refuge -- 3.4.4 AMR abundance linear relationship with soil chemical components -- 3.4.5 Core resistome: high abundance, low diversity -- 3.5 Discussion -- 3.5.1 Soil chemical components driving AMR gene abundance -- 3.5.2 Refuge resistome disparity: unveiling the role of AMR genes and microbial composition -- 3.5.3 widespread occurrence and implication of glycopeptide antibiotic resistance -- 3.5.4 The core resistome: a foundation of antibiotic resistance across refuges -- 3.5.5 Divergent patterns of AMR gene prevalence compared to global studies -- 3.5.6 Future considerations: climate change and the evolving resistome in high-latitude soils -- 3.5.7 Limitations -- 3.6 Conclusion -- 3.7 Funding & acknowledgements -- 3.8 References. Chapter Four: General conclusion -- 4.1 References. Apendix A: Supplementary figures and tables
A range extension for Carex sartwellii in Interior Alaska
Full text linkThesis (M.S.) University of Alaska Fairbanks, 2024Mean annual temperatures and growing season length have been increasing in northern latitudes. This has impacted permafrost thaw and the water balance of northern regions, resulting in a pattern of drying lakes in the Yukon Flats, Alaska. As lakes dry, they expose lake sediments to colonization by terrestrial vegetation. Recent interest in the terrestrial response to climate change and its effects on ecosystem services led to the formation of the Yukon River Basin project. As a part of this project, we studied plant succession and diversity in the drying lake basins. In the course of our field work we encountered a sedge we believed to be previously undocumented in Alaska. Our documentation of Sartwell’s Sedge, Carex sartwellii, on nine drying lakes during fieldwork in the central Yukon Flats, Alaska, represents a range extension for this species. Previously, its range extended as far northwest as Yukon, Canada, with a reported, but lost collection, from Alaska in 1895. Two earlier collections from the Yukon Flats have been verified; one was misidentified as Carex praegracilis until 2007. Carex sartwellii’s assumed absence from Alaska and Yukon flora, misidentification of an earlier collection, and the remoteness of the Yukon Flats may have contributed to the rarity of its collection. In Alaska this species is morphologically similar to C. praegracilis, but can be distinguished using traits of the perigynia, leaf sheaths, and the production of true vegetative culms. This sedge was found extensively in alkaline drying lake basins, which are similar environments to those found during the Pleistocene. Many of the species that occurred with C. sartwellii in lake basin plant communities have been documented in paleo reconstructions of plants from the Beringian steppe. The Yukon Flats are botanically understudied as a region in Alaska and further research should focus on identifying these unique relict plant communities in the Yukon Flats and their distribution along historic Beringia into Yukon. This would likely lead to more collections of C. sartwellii and expand our knowledge of its distribution and ecology.cooperative agreement (RWO180) from the United States Geological Survey’s Alaska Science Center to the University of Alaska Fairbanks, Bonanza Creek Long-term Ecological Research program (funded jointly by National Science Foundation grant DEB-0423442 and United States Department of Agriculture’s Forest Service, Pacific Northwest Research Station grant PNW01-JV-11261932Chapter 1: General introduction -- 1.1 References. Chapter 2: A range extension for Carex sartwellii in Interior Alaska -- 2.1 Abstract -- 2.2 Introduction -- 2.3 History of collection of Carex sartwellii in Alaska and Yukon -- 2.4 Ecology -- 2.4.1 Yukon Flats -- 2.4.2 Shrinking lakes -- 2.5 Morphology -- 2.6 Conclusion -- 2.7 References. Chapter 3: General conclusions -- 3.1 References
Perceived Barriers and Facilitators to Food Security in Ketchikan Alaska
Full text linkA Project Submitted in Partial Fulfillment of the Requirements
for the Degree of
MASTER OF SCIENCE
in
Dietetics and NutritionKetchikan, Alaska is Alaska's First City and is famously known as the Salmon Capital of the world. Ketchikan is Lingít Aaní, the ancestral land of the Taantʼá Ḵwáan and Saanya Ḵwáan people of Revillagigedo Island.1 Ketchikan Gateway Borough is home to 13,754 residents.2 Being located on an island presents unique challenges to the residents regarding food security. Food that is not harvested or grown locally is shipped via barge from Seattle, WA. Limited published research exists regarding food security in Alaska, and primary research on food security in Ketchikan is nonexistent. The goal of this study is to analyze food insecurity and related variables in Ketchikan, AK. The study’s objectives are to measure food insecurity using results from an online survey, identify the most prevalent perceived barriers and facilitators to food security, and determine potential associations between food security status and barriers/facilitators to food security in Ketchikan, AK. This study utilized a retrospective (the past 12 months) cross-sectional study design to ascertain perceived barriers and facilitators to food security in Ketchikan, Alaska. A one-time, electronic survey was made available on Qualtrics and advertised via flyers, social media, and tables at a grocery store. Chi-square analyses were used to determine significant (p < 0.05) associations between food security status and perceived barriers and facilitators. The total sample analyzed was 108 Ketchikan residents. A significant relationship was found between food security status and access to transportation, sufficient money, the availability of meat, avoiding the grocery store: not due to COVID-19, receiving food from food bank, etc. and expense of food.Abstract / Table of Contents / List of Tables / List of Figures / List of Appendices / Acknowledgements / Introduction / Literature Review / Methods / Results / Discussion / Strengths and Limitations / Dietetics and Nutrition Practice Implications / References / Appendice
UAS Facilities Services News Letter
Full text linkLearn the basics -- Bollard replacement project -- Become a UAS shuttle driver -- Trades crew -- Lighting upgrades on campus -- Lighting upgrades TEC -- Office refresh -- Grounds & Landscaping -- Grounds crew -- Did you know? -- Custodial crew -- October is domestic violence awareness month -- Noyes Pavilion renovation -- Facilities planning & construction project updates -- Áakʼw Tá Hít -- New project manager -- Security cameras -- Ketchikan Maritime Center -- Lakeside Grill refresh -- Housing Lodge fuel tank replacement -- Sneeze guard greenhouse -- Anderson Building renovations -- Housing concrete sidewalk repair -- Welding Lab / Fire alarm replacement -- NSRL / Relocation -- UAS Ketchikan Paul Bldg. / Nursing project -- Grades are in -- Reporting facility problems -- Greetings from Sitka -- Snow prep work -- Sitka facilities projects -- Canopy project is underway -- Room remodel getting rolling -- Migration to a new building controls system is happening behind the scenes -- Sending and receiving mai
Isotopic, geochemical and petrographic analysis of the Otuk Formation, Northern Alaska
Full text linkThesis (M.S.) University of Alaska Fairbanks, 2024The Triassic-Jurassic boundary is associated with one of the big five Phanerozoic mass extinction events and is characterized by global negative δ13C excursions, indicating a major disruption in the carbon cycle. The end-Triassic extinction event was caused by Central Atlantic Magmatic Province volcanism, that initiated the breakup of the supercontinent Pangea. Abundant greenhouse gas emissions, including CO2 and CH4, from the volcanic activity, affected multiple environmental factors. Global warming, ocean acidification, deoxygenation, mass mortality, and lithological change are documented across the boundary. These environmental fluctuations are also observed due to human-induced global climate change, making understanding the end-Triassic extinction significant. Northern Alaska during the Late Triassic has evidence of being the location of an upwelling zone, influencing redox conditions on the sea floor. I hypothesize that isotopic, geochemical and petrographic analyses into Northern Alaska’s Late Triassic Otuk Formation will give a better understanding of the depositional environments in which it formed. Our research has documented the Triassic-Jurassic boundary using carbon and nitrogen isotopes in the rock record, where previously it was not well recorded in Alaska. Research into the Otuk Formation also helped identify the high petroleum potential of these organic-rich rocks. Late-Triassic Northern Alaska rocks were deposited in marine oxic to anoxic conditions, impacting organic burial and paleo¬ redox conditions. Paleo-redox conditions of euxinic environments were identified through the presence of pyrite framboids. A negative carbon isotope excursion was identified in the Otuk Formation, also corresponding with a change in lithofacies and fossil size and abundance. Sedimentary petrology and TOC values documented environmental changes from oxic bivalve¬ rich facies to dark, low-oxygen, organic shales across the Triassic-Jurassic boundary. The Triassic- Jurassic boundary is observed in Northern Alaska, and can act as a marker for multiple environmental changes at that time.The American Association of Petroleum Geologists (AAPG) through the John E. Kilkenny Memorial Grant and The Geological Society of America (GSA)Chapter 1: Geological background. Chapter 2: Introduction -- 2.1 Scientific significance -- 2.2 Otuk Formation -- 2.2.1 Shale member -- 2.2.2 Chert member -- 2.2.3 Limestone member -- 2.2.4 Blankenship member -- 2.2.5 Otuk Formation background -- 2.3 Shublik Formation -- 2.4 Oxygen settings and upwelling zones -- 2.5 End-Triassic extinction event -- 2.6 Nitrogen cycle -- 2.7 Redox reactions -- 2.7.1 Phosphorous -- 2.7.2 Pyrite -- 2.8 Trace metals. Chapter 3: Methods -- 3.1 Data -- 3.2 Isotope geochemistry -- 3.2.1 Carbon isotope geochemistry -- 3.2.2 Nitrogen isotope geochemistry -- 3.3 Organic chemistry -- 3.3.1 Total Organic Carbon (TOC) -- 3.4 Sedimentary petrology -- 3.5 Scanning Electron Microscopy (SEM). Chapter 4: Results -- 4.1 Otul Formation stratigraphic sections -- 4.2 Carbon and nitrogen isotope geochemistry results -- 4.3 Rock-eval pyrolysis results -- 4.4 Total Organic Carbon results -- 4.5 Biostratigraphic review -- 4.6 Sedimentary petrology and lithology results -- 4.7 Scanning electron microscopy results. Chapter 5: Discussion -- 5.1 The Triassic-Jurassic boundary documented in the Otuk Formation -- 5.2 Petroleum sources. Chapter 6: Conclusion. References. Appendices
Know Your Tsunami Hazard in Seldovia
Full text linkCoastal Alaska communities live with the most serious tsunami hazard in the United States. The Alaska Earthquake Center helps coastal communities prepare for the next tsunami disaster. We provide state and local officials with the best available scientific information for addressing the variety of tsunami hazards faced by their communities. These community-specific brochures distill information from several scientific publications, such as tsunami inundation reports, pedestrian travel time maps, and maritime response guidance, into a handy, quick reference. The brochures include maps with community-designated safety information, historical tsunami information, as well as links for local and statewide tsunami preparedness information. The brochures are rack-card size for easy display, and a great safety resource for both locals and visitors.
The Earthquake Center partnered with the Alaska Division of Homeland Security and Emergency Management, the City of Seldovia, and Seldovia Village to create this brochure, tailoring the map, safety contact information, and historical information to this location
Divergence and adaptation in Beringian birds
Full text linkThesis (M.S.) University of Alaska Fairbanks, 2024Beringia is a high-latitude hotspot of avian divergence and speciation. The unique biogeography of Beringia impacted avian speciation in two ways: through the cyclic appearance of the land bridge between the Asian and North American continents and through glacial refugia. These cyclic processes repeatedly split and connected avian populations, alternately reducing and increasing opportunities for gene flow between populations. In this thesis, I examine how this dynamic system impacted Beringian avian taxa using population genomic analyses. First, I examine broad patterns of divergence and gene flow across 11 lineages of birds using ultraconserved elements (UCEs), which are a multi-locus subsampling of the nuclear genome. These bird lineages contain two or more sister taxa at the population, subspecies, or species level that were likely impacted by the Bering land bridge and/or by glacial refugia. I tested models that provided key demographic information, such as population size, gene flow, and divergence time estimates. Demographic modeling showed gene flow in all cases at a wide range of rates between pairwise comparisons, and all inferred models included a divergence event during the Quaternary. Next, I focus on one species, the Song Sparrow (Melospiza melodia), in the Beringian part of its range. Five subspecies of the Song Sparrow reside in southern Alaska, from the Aleutian Islands to southeast Alaska, and have a wide range of body sizes. Using whole- genomic sequencing and morphology, I examine the phenotypic and genomic differences in these subspecies. I quantified the morphological differences, showing that the western subspecies are significantly larger than the eastern subspecies. I then determined that two candidate genes are under positive selection in the most isolated subspecies, M. m. maxima. Finally, I reconstructed a phylogeny and found that M. m. maxima is sister to the other M. melodia subspecies. These results highlight how the unique biogeography of Beringia impacted the generation of avian diversity in the region.Kessel Fund for Northern Ornithology and the Friends of OrnithologyChapter 1: General introduction -- Chapter 2: Gene flow accompanies divergence in Beringian birds -- Chapter 3: Evidence of positive selection and a novel phylogeny among five subspecies of song sparrow (Melospiza melodia) in Alaska -- Chapter 4: General conclusions
Bellwethers of change: population modelling of North Pacific humpback whales from 2002 through 2021 reveals shift from recovery to climate response
Full text linkFor the 40 years after the end of commercial whaling in 1976, humpback whale populations in the North Pacific Ocean exhibited a prolonged period of recovery. Using mark–recapture methods on the largest individual photo-identification dataset ever assembled for a cetacean, we estimated annual ocean-basin-wide abundance for the species from 2002 through 2021. Trends in annual estimates describe strong post-whaling era population recovery from 16 875 (± 5955) in 2002 to a peak abundance estimate of 33 488 (± 4455) in 2012. An apparent 20% decline from 2012 to 2021, 33 488 (± 4455) to 26 662 (± 4192), suggests the population abruptly reached carrying capacity due to loss of prey resources. This was particularly evident for humpback whales wintering in Hawai‘i, where, by 2021, estimated abundance had declined by 34% from a peak in 2013, down to abundance levels previously seen in 2006, and contrasted to an absence of decline in Mainland Mexico breeding humpbacks. The strongest marine heatwave recorded globally to date during the 2014–2016 period appeared to have altered the course of species recovery, with enduring effects. Extending this time series will allow humpback whales to serve as an indicator species for the ecosystem in the face of a changing climate.NOAA Fisheries.
Eric and Wendy Schmidt Family Foundation.
Cheeseman's Ecology Safaris.
Cascadia Research Collective.
The Marine Mammal Center.
The Hurtigruten Foundation.
Defenders of Wildlife.
Individual Supporters of Happywhale.Abstract -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- 5. Conclusion -- Ethics -- Data accessibility -- Declaration of AI use -- Authors' contributions -- Conflict of interest declaration -- Funding -- Acknowledgements -- References -- Supplemental material -- Supplementary information.Ye
Snow avalanches are a primary climate-linked driver of mountain ungulate populations
Full text linkSnow is a major, climate-sensitive feature of the Earth’s surface and catalyst of fundamentally important ecosystem processes. Understanding how snow influences sentinel species in rapidly changing mountain ecosystems is particularly critical. Whereas effects of snow on food availability, energy expenditure, and predation are well documented, we report how avalanches exert major impacts on an ecologically significant mountain ungulate - the coastal Alaskan mountain goat (Oreamnos americanus). Using long-term GPS data and field observations across four populations (421 individuals over 17 years), we show that avalanches caused 23−65% of all mortality, depending on area. Deaths varied seasonally and were directly linked to spatial movement patterns and avalanche terrain use. Population-level avalanche mortality, 61% of which comprised reproductively important prime-aged individuals, averaged 8% annually and exceeded 22% when avalanche conditions were severe. Our findings reveal a widespread but previously undescribed pathway by which snow can elicit major population-level impacts and shape demographic characteristics of slow-growing populations of mountain-adapted animals.Alaska Climate Adaptation Science Center. Alaska Department of Fish and Game. Federal Aid in Wildlife Restoration Program. Alaska Department of Transportation and Public Facilities. Alaska Division of Geological and Geophysical Surveys. Bureau of Land Management. City of Sitka. Coeur Alaska. Federal Highway Administration. Wild Sheep Foundation.Abstract -- Introduction -- Results -- Discussion -- Methods -- Data availability -- Code availability -- References -- Acknowledgements -- Author information -- Ethics declarations -- Peer review -- Additional information -- Supplementary information -- Rights and permissions -- About this article -- CommentsYe
Trophic stability and change across a sea ice cover gradient on the western Antarctic Peninsula
Full text linkThe western Antarctic Peninsula (AP) is experiencing significant changes to sea ice cover, altering the macroalgal cover and potentially affecting the foundation of benthic food webs. We used fatty acid signatures as dietary and physiological trophic biomarkers to test the hypothesis that a gradient of 36-88% mean annual ice cover would affect the trophic ecology of fleshy macroalgae and diverse benthic invertebrate consumers along the western AP. We used SCUBA to collect organisms from benthic rocky nearshore habitats, 5-35 m depth, at 15 study sites during April-May of 2019. There were no consistent ecosystem-scale differences in the nutritionally important polyunsaturated fatty acids or other univariate fatty acid summary categories in either the seaweeds or invertebrates across the ice gradient, but we did find site-level differences in the multivariate fatty acid signatures of all seaweeds and invertebrates. Ice cover was a significant driver of the fatty acid signatures of 5 invertebrates, including 3 sessile (an anemone, a sponge, and a tunicate) and 2 mobile consumers (a sea star and a sea urchin). The multivariate fatty acid signatures of 2 other sea stars and a limpet were not affected by the ice gradient. These results indicate that the trophic ecology and resource assimilation of sessile consumers that are more connected to the macroalgal-derived food web will be more sensitive than mobile consumers to impending changes to annual ice and macroalgal cover along the western AP.National Science Foundation.Abstract -- Key words -- 1. Introduction -- 2. Materials and methods -- 3. Results -- 4. Discussion -- 5. Conclusions -- Acknowledgements -- Literature CitedYe