Microbial ecology and biodegradation potential of a sulfolane-contaminated, subarctic aquifer

Thesis (Ph.D.) University of Alaska Fairbanks, 2019Contaminant biodegradation is one of many ecosystem services aquifer microbiota can provide to humans. Sulfolane is a water-soluble emerging contaminant that is associated with one of the largest contaminated groundwater plumes in the state of Alaska. Despite being widely used, the biodegradation pathways and environmental fate of sulfolane are poorly understood. In this study, we investigated the biodegradation of sulfolane by the microbial community indigenous to this contaminated subarctic aquifer in order to better understand the mechanisms and rates of loss, as well as the environmental factors controlling them. First, we conducted aerobic and anaerobic microcosm studies to assess the biodegradation potential of contaminated subarctic aquifer substrate and concluded that the aquifer microbial community can readily metabolize sulfolane, but only in the presence of oxygen, which is at low concentration in situ. We also investigated the impacts of nutrient limitations and hydrocarbon co-contamination on sulfolane biodegradation rates. To identify exactly which community members were actively degrading sulfolane, we combined DNA-based stable isotope probing (SIP) with genome-resolved metagenomics methods. We found a Rhodoferax sp. to be the primary sulfolane degrading microorganism in this system and obtained a near-complete genomic sequence of this organism, which allowed us to propose a new metabolic model for sulfolane biodegradation. Finally, we assessed the distribution of sulfolane-degrading bacteria throughout the contaminated subarctic aquifer by sequencing 16S rRNA genes from 100 groundwater samples and two sulfolane treatment systems and screening for the sulfolane degrader previously identified using SIP. This assessment revealed that sulfolane biodegradation potential is widespread throughout the aquifer but is not likely occurring under normal conditions. However, the sulfolane-metabolizing Rhodoferax sp. was the most dominant microbe in an effective experimental air-sparge system, suggesting that injecting air into the aquifer can stimulate sulfolane biodegradation in situ. These studies are the first to investigate sulfolane biodegradation potential in a subarctic aquifer. Through this work, we learn there are several important factors limiting biodegradation rates, we expand the known taxonomic distribution of sulfolane biodegradation, and we shed insights into the mechanisms underlying an effective in situ sulfolane remediation system.Alaska Department of Environmental Conservation and an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM10339

Development of Resting Cell Assay Protocol to Characterize Sulfolane Degrading Bacteria

Sulfolane is a chemical contaminant present in hundreds of commercial and residential drinking wells in the North Pole area. Due to the possible health impacts of consumption, degradation/removal of the sulfolane from contaminated wells is necessary. Microbial isolates taken from sulfolane contaminated sites have shown the potential to degrade sulfolane. It is the purpose of my research to design a protocol by which sulfolane tolerant bacteria could be screened or their potential to utilize sulfolane as a sole carbon source (SOCS), and characterize them as sulfolane degraders

Plant succession in the Arctic Brooks Range: floristic patterns from alpine to foothills, along a glacial chronosequence and elevation gradient

Thesis (M.S.) University of Alaska Fairbanks, 2019In the wake of rapid glacial retreat, alpine habitats in the Arctic are expanding as freshly exposed surfaces become vegetated. Many glaciers in alpine cirques have nearly disappeared, and little is known about the rate of colonization or pioneer communities that develop following deglaciation. Newly developed habitats may provide refugia for sensitive Arctic flora and fauna, especially in light of polar warming. To assess this process, vegetation communities developing on two recently deglaciated moraines in the Central Brooks Range were surveyed and compared with communities along a transect spanning both a glacial chronosequence (40-125,000 years since deglaciation) and an elevation gradient (1700-500 m) into the Arctic foothills. Results show that primary succession begins almost immediately following deglaciation. Within forty years fine-grained and rock substrates hosted small communities of 8-13 vascular and nonvascular plant species. Many pioneer taxa, especially lichens, persist into later stages of succession. Overall succession is directional and slow, increasing in species richness for about 10,000 years, after which richness decreases and communities stabilize. This is the first vegetation study on primary succession in the high Central Brooks Range, providing a missing link to a vegetation transect along the Arctic Bioclimatic gradient

Long-term legacy of phytoremediation on plant succession and soil microbial communities in petroleum-contaminated sub-Arctic soils

Phytoremediation can be a cost-effective method of restoring contaminated soils using plants and associated microorganisms. Most studies follow the impacts of phytoremediation solely across the treatment period and have not explored long-term ecological effects. In 1995, a phytoremediation study was initiated near Fairbanks, Alaska, to determine how the introduction of annual grasses and/or fertilizer would influence degradation of petroleum hydrocarbons (PHCs). After 1 year, grass and/or fertilizer-treated soils showed greater decreases in PHC concentrations compared to untreated plots. The site was then left for 15 years with no active site management. In 2011, we re-examined the site to explore the legacy of phytoremediation on contaminant disappearance, as well as on plant and soil microbial ecology. We found that the recruited vegetation and the current bulk soil microbial community structure and functioning were all heavily influenced by initial phytoremediation treatment. The number of diesel-degrading microorganisms (DDMs) was positively correlated with the percentage cover of vegetation at the site, which was influenced by initial treatment. Even 15 years later, the initial use of fertilizer had significant effects on microbial biomass, community structure, and activity. We conclude that phytoremediation treatment has long-term, legacy effects on the plant community, which, in turn, impact microbial community structure and functioning. It is therefore important to consider phytoremediation strategies that not only influence site remediation rates in the short-term but also prime the site for the restoration of vegetation over the long-term.</p

Tissue Specific Gene Expression In Chelydra Serpentina

Epigenetic regulation has been studied in mammals, but research in reptiles is lacking. Knowing where specific genes are expressed is the first step to examining epigenetic regulation of tissue specific and cell-type specific gene expression. Differences in gene expression allude to differences in gene regulation and gene function and will require further study. In order to address the question of tissue specific gene expression, we review literature on embryonic development, sex determination, and specific genes that display tissue specific or cell-type specific expression patterns. Next, we review what is known about regulation of gene expression in reptiles. We then outline the protocol used to examine expression patterns of Anti-Müllerian hormone, Dmrt1, Sox9, FoxL2, Somatostatin, Growth hormone, Cdx1, and Slc12a1 in the common snapping turtle. Finally, we compare these expression patterns to those found in mammals and discuss any observed differences

Factors limiting sulfolane biodegradation in contaminated subarctic aquifer substrate.

Sulfolane, a water-soluble organosulfur compound, is used industrially worldwide and is associated with one of the largest contaminated groundwater plumes in the state of Alaska. Despite being widely used, little is understood about the degradation of sulfolane in the environment, especially in cold regions. We conducted aerobic and anaerobic microcosm studies to assess the biological and abiotic sulfolane degradation potential of contaminated subarctic aquifer groundwater and sediment from Interior Alaska. We also investigated the impacts of nutrient limitations and hydrocarbon co-contamination on sulfolane degradation. We found that sulfolane underwent biodegradation aerobically but not anaerobically under nitrate, sulfate, or iron-reducing conditions. No abiotic degradation activity was detectable under either oxic or anoxic conditions. Nutrient addition stimulated sulfolane biodegradation in sediment slurries at high sulfolane concentrations (100 mg L-1), but not at low sulfolane concentrations (500 μg L-1), and nutrient amendments were necessary to stimulate sulfolane biodegradation in incubations containing groundwater only. Hydrocarbon co-contamination retarded aerobic sulfolane biodegradation rates by ~30%. Our study is the first to investigate the sulfolane biodegradation potential of subarctic aquifer substrate and identifies several important factors limiting biodegradation rates. We concluded that oxygen is an important factor limiting natural attenuation of this sulfolane plume, and that nutrient amendments are unlikely to accelerate biodegradation within in the plume, although they may biostimulate degradation in ex situ groundwater treatment applications. Future work should be directed at elucidating the identity of indigenous sulfolane-degrading microorganisms and determining their distribution and potential activity in the environment

Sulfolane concentration over time in aerobic microcosm incubations.

<p>(A) Sulfolane biodegradation is nutrient limited in high concentration sediment slurry microcosms. (B) Sulfolane biodegradation is not nutrient limited in low concentration sediment slurry microcosms. (C)Hydrocarbon co-contamination retards the rate of sulfolane biodegradation in sediment slurry microcosms. (D) Nutrient amendment is necessary to stimulate sulfolane biodegradation in groundwater only microcosms. Live slurries contained an active microbial community and sulfolane. Sterile controls were heat-killed. (N) indicates amendment with a dilute mineral nutrient solution. (H) indicates treatments amended with hydrocarbons. (O) indicates treatments amended with a complex organic nutrient solution. Error bars indicate standard deviation from the mean.</p

Long-term legacy of phytoremediation on plant succession and soil microbial communities in petroleum-contaminated sub-Arctic soils

&lt;jats:p&gt;Abstract. Phytoremediation can be a cost-effective method of restoring contaminated soils using plants and associated microorganisms. Most studies follow the impacts of phytoremediation solely across the treatment period and have not explored long-term ecological effects. In 1995, a phytoremediation study was initiated near Fairbanks, Alaska, to determine how the introduction of annual grasses and/or fertilizer would influence degradation of petroleum hydrocarbons (PHCs). After 1 year, grass and/or fertilizer-treated soils showed greater decreases in PHC concentrations compared to untreated plots. The site was then left for 15 years with no active site management. In 2011, we re-examined the site to explore the legacy of phytoremediation on contaminant disappearance, as well as on plant and soil microbial ecology. We found that the recruited vegetation and the current bulk soil microbial community structure and functioning were all heavily influenced by initial phytoremediation treatment. The number of diesel-degrading microorganisms (DDMs) was positively correlated with the percentage cover of vegetation at the site, which was influenced by initial treatment. Even 15 years later, the initial use of fertilizer had significant effects on microbial biomass, community structure, and activity. We conclude that phytoremediation treatment has long-term, legacy effects on the plant community, which, in turn, impact microbial community structure and functioning. It is therefore important to consider phytoremediation strategies that not only influence site remediation rates in the short-term but also prime the site for the restoration of vegetation over the long-term. &lt;/jats:p&gt

Plant succession on glacial moraines in the Arctic Brooks Range along a >125,000-year glacial chronosequence/toposequence

ABSTRACTWidespread glacial retreat is now occurring in many arctic mountain ranges, yet little is known about primary succession following deglaciation in these settings. Newly created habitats could provide refugia for flora and fauna whose ranges are threatened elsewhere by rapid warming. To assess vegetation responses to glacial retreat in an arctic–alpine setting, we first describe plant community development on two recently deglaciated moraines in the Brooks Range. We then compare these recent communities with communities developed along a moraine chronosequence that spans >125,000 years and ranges in altitude between 800 and 1,700 m.a.s.l. Results show that (1) within twenty-two to thirty-six years following deglaciation, primary succession begins with the assembly of small communities of eight to thirteen vascular and nonvascular plant species; (2) species turnover is low, with many pioneer taxa, particularly lichens, persisting at the oldest sites and across all altitudes; and (3) overall, succession is directional and slow, with species richness increasing for up to 25,000 years, and percentage vegetation cover reaching >100 percent on the oldest glacial deposits. This is the first vegetation study on primary succession in the high central Brooks Range, and it supplies a previously missing alpine element within a vegetation transect across northern Alaska’s bioclimatic gradient