Theses @ Nicholls State University

 
Abstract
The Diamondback Terrapin (Malaclemys terrapin) is a brackish water turtle with a range spanning from the north-western Atlantic coast through the western Gulf Coast of Texas. Although well-studied along the Atlantic portion of their range, studies of Louisiana terrapin are lacking and only in the last decade have studies on local populations been produced. To further expand the knowledge of Louisiana’s terrapins, a mark-recapture study was conducted with turtles at Elmer's Island Wildlife Refuge and East Grand Terre. Un-baited fyke nets were used to capture terrapin from March through August 2021. Survey efforts resulted Ein 81 total capture events of 79 unique individuals and 2 within-season recaptures. Sex ratios at both study locations were female-biased and females were significantly larger than males in all morphometrics. Using my capture history data and previous survey data I was able to estimate population parameters for East Grand Terre. The model-averaged super population estimate was 720 individuals. Furthermore, model-averaged survival and capture probabilities ranged from 0.4–1.0 and 0.04–0.8, respectively. This study effectively established sampling protocol and produced baseline data for incorporation into subsequent seasons of data analysis for an area impacted by the 2010 Deepwater Horizon oil spill and coastal land loss over the last 50 years. Continuing such long-term study of these populations is pivotal for increasing sample size and statistical power, providing insight into the morphometric and population structures of Louisiana terrapin populations, and monitoring population demographics in the wake of local and climate-induced stressors.

 
Abstract
Aquatic invasive species are a major issue worldwide that global biodiversity and disrupt economic systems. It is therefore important to develop strategies and technologies to resist the dispersal and impacts of aquatic invaders. Apple Snails (Ampullaridae) from the genus Pomacea are large, freshwater snails with a native distribution from Argentina to Florida. Several traits have made Apple Snails successful in establishing invasive populations across the world. Invasive Pomacea species voraciously consume macrophytes, leading to ecosystem disturbance and reduced aquacultural profits. In the United States, Pomacea maculata has become established across the Gulf coast from Texas to southern Florida and northward along the Atlantic coast to South Carolina. Apple Snail populations in southern Louisiana are particularly problematic because of the threat they pose to natural aquatic ecosystems, and rice and crayfish aquaculture. Apple Snails also impact public health, by serving as a paratenic host to Rat Lungworm Angiostrongylus cantonensis, an invasive, human disease-causing parasite. The ecological, environmental, and public health costs from P. maculata invasions in the U.S. may increase, yet management efforts have had little success in eradicating populations or limiting range expansion. I used population genetic and morphometric analyses to assess population connectivity and morphometric relationships among habitat variables to better understand Apple Snail ecology in Louisiana.. I also used a qPCR assay to test snails from Veret Canal and Bayou Chevreuil for Rat Lungworm. Analysis of genetic diversity of 134 snails across 7 sampling locations revealed high diversity and clear population structure among all 4 sampling sites in Terrebonne Estuary and snails from Barataria Preserve. Bayou Segnette appeared to be an intermediate population with admixture from both the Terrebonne population and Barataria Preserve. Structure appeared to be mediated by active dispersal at small scales and by iv anthropogenic dispersal at large scales. Genetic distances were significant but smaller than those observed for P. maculata populations in South Carolina and Georgia, the only other populations studied in the United States, suggesting greater total gene flow across Apple Snail populations in Louisiana. These findings suggest Apple Snail populations in Louisiana may be structured by hydrologic basin and also by anthropogenically mediated dispersal. This study provides the foundation necessary to develop targeted genetic studies to address management goals. Rat Lungworm was not detected in any samples (n=50), indicating a reduction in prevalence in the New Orleans area. Mean snail size (mm) varied across sampling locations and was affected by habitat permanence but not by flow or substrate. These results suggest that habitat permanence affects average snail size and may affect the impact of herbivory at small scales.

 
Abstract
The presence of xenobiotic compounds in the environment is a major concern for human and wildlife health. The removal of these hazardous compounds, such as phenol, is crucial in limiting potential exposure to toxicity. The purpose of this study is to measure the efficiency of a bacterial consortium’s ability to degrade phenol. The consortium was obtained from sediment that polluted the yards of residential properties in southeastern Louisiana after Hurricane Ida in August 2021. Four multidrug resistant bacteria including Proteus mirabilis, Bacillus cereus, Bordetella avium, and Pseudomonas aeruginosa isolated from the sediment were tested for their tolerance to high phenol concentration. All four bacterial isolates were able to grow in the presence of 1,000 mg/L of phenol under co-metabolic condition but were unable to degrade phenol. A bacterial consortium was developed through an enrichment technique and this consortium was able to use phenol as the sole carbon source and degraded phenol. The consortium was able to remove more than 95% of phenol within 14 days when the phenol concentration was 100 mg/L. However, phenol degradation efficiency decreased when the phenol concentration was increased in the culture medium. The consortium removed 30% of phenol at a high concentration of 1,000 mg/L. The consortium was dominated by three distinct phyla and nine distinct genera. The dominant phylum was represented by Proteobacteria and the dominant genus in the consortium was Shigella. The consortium removed phenol via β-ketoadipate pathway with the production of the following metabolites, catechol, cis,cis-muconic acid, succinate, and fumarate. The novelty of this study was the high tolerance of phenol concentration of 1,000 mg/L by the bacterial consortium and its ability to degrade phenol. This is one of the highest phenol concentrations reported in the literature. The bacterial consortium could serve as a biocatalyst to remove phenol from the phenol polluted sites.

 
Abstract
Vegetation in saltmarsh habitats face stressors including those imposed by human activities, such as oil spills. This is highlighted by the occurrence of the Deepwater Horizon spill, the largest oil spill in the United States to date, which impacted coastal habitats along northern Gulf of Mexico. Understanding ecological damage from oiling in coastal wetlands necessitates study of how oiling impacts important species in these habitats; however, comparatively little is known about the oiling responses of high marsh vegetation. For instance, the effects of oiling on Avicennia germinans have been addressed in a number of observational and controlled studies, but knowledge gaps exist regarding the potential interactive effects of soil and aboveground tissue oiling on A. germinans seedlings. Further, the impacts of oiling on Batis maritima have not yet been experimentally assessed. A greenhouse study was performed with the goal of determining the effects of both soil oiling and aboveground tissue oiling by MC252 oil on health, morphology and growth responses of A. germinans and B. maritima seedlings in a controlled setting. Specifically, a 2 species x 4 soil oiling levels x 3 tissue oiling levels factorial design was implemented at the Nicholls State University Farm greenhouse facility. Short and long-term growth indicators were measured over the duration of the study from early June 2018 to late October 2018. Significant reductions in several growth responses were detected under the highest level of soil oiling (4 L m-2) for B. maritima, whereas tissue oiling was found to impact only B. maritima stem diameter and under 100% tissue coverage. In contrast, no discernable impact to A. germinans growth was discerned in this study apart from specific leaf area being significantly higher for 100% tissue oiling compared to no tissue oiling, corroborating previous research that suggested tolerance to oiling at comparable levels by this species. In contrast, B. maritima was notably susceptible to the highest level of soil oiling employed in this study. Overall, this research has elucidated differential oiling tolerances of two important coastal species in the Northern Gulf of Mexico.

 
Abstract
The lower Barataria estuary in southeast Louisiana is a natural, commercially harvested area for the Eastern Oyster, Crassostrea virginica. Due to numerous environmental and anthropogenic stressors, the creation of permanent and commercially temporary reefs have been implemented by bedding crushed concrete cultch material as an alternative medium to oyster shell for oyster attachment and commercial development. Cultch reefs offer multi-dimensional ecological benefits including protection of adjacent shorelines from coastal erosion, solid substrate for larval oyster attachment, increased habitat for aquatic community development and oyster population development. The purpose of this project was to determine if increasing crushed concrete cultch density increases populations of oysters and other reef communal organisms. Constructed reefs at the Canal (1.5 hectares) and Pond (2.1 hectares) sites within the Wisner Property were selected as suitable subtidal locations for concrete reef restoration and bedded cultch was randomly sampled to determine experimental cultch densities. Community structure, oyster maturation, and oyster growth was assessed quarterly, and water quality and larval oyster recruitment data was recorded monthly to indicate reproductive events and hydrologic resiliency. Forty-eight cultch cages (12 cages per density treatment) with four different crushed concrete densities (no cultch, 2 L/0.37 m2, 5 L/0.37 m2, and 14 L/0.37 m2) were deployed in October 2018 at the Pond site. Additionally, a small hand dredge was used to collect oysters on bedded cultch at Canal and Pond sites. Mean oyster density in cultch cages increased with increasing cultch density, however, a significant difference in oyster density was only observed between reference and LDWF cages (H3 = 12.86; P = 0.005). Additionally, oyster shell height (SH) was significantly larger in reference cages (37.84 ± 1.81 mm) compared to LDWF cultch density cages (30.68 ± 0.91 mm; H3= 10.11, P = 0.018). Collectively 54.5% of C. virginica sampled on bedded cultch at Canal and Pond sites exceeded commercial harvest size (SH ≥ 75 mm). Constructed cultch reefs at Canal and Pond sites supported recruitment and growth of C. virginica to commercial size within 18 months. Created interstitial space from constructed reefs allowed for significant increases in species richness with increased cultch density (F3,44 = 2.86, P = 0.048). Total dry-weight biomass increased with increasing cultch density and LDWF density cages had significantly more total dry-weight biomass compared to reference cages (H3 = 17.82, P < 0.001). Results from this study indicates that constructed concrete cultch reefs are successful in Louisiana subtidal estuaries for increasing oyster and faunal densities. Understanding the relationships among oyster density, recruitment, and community structure on crushed concrete cultch is important for future oyster and coastal restoration projects in Louisiana estuarine habitats impacted by coastal land loss and commercial overharvest.

 
Abstract
Belowground biomass is a key component of ecosystem structure that contributes to wetland stability by mediating erosion resistance and vertical accretion. This study examined the relationship between belowground biomass, soil shear strength, and carbon sequestration at 37 wetland sites across Louisiana, representing five wetland types: salt marsh (n = 7), brackish marsh (n = 10), intermediate marsh (n = 6), fresh marsh (n = 7), and forested wetlands (n = 7). Belowground biomass was collected using a 7.65-cm diameter by 30-cm long soil corer and sectioned into 0-15 cm and 15-30 cm soil depth increments. Soil shear strength was measured in triplicate at the mid-point of each soil depth increment using a shear vane with an attached torque gauge. A second set of soil cores was collected to a depth of 1 m using a 5-cm diameter semi-cylindrical corer and analyzed for 137Cs-based accretion, carbon content, and bulk density to enable the determination of soil carbon accumulation. In general, belowground biomass increased with increasing salinity, however, live root biomass was greatest in forested wetlands. Soil shear strength was significantly higher in forested wetlands compared to other wetland types. Soil carbon accumulation was significantly lower in forested wetlands compared to other wetland types, which had similar mean soil carbon accumulation. In forested wetlands, soil shear strength was negatively correlated with both live and total belowground biomass. Fresh and intermediate marsh soil shear strength was positively correlated with live and total belowground biomass. In fresh and brackish marsh, soil carbon had a negative correlation with belowground biomass. Forested wetlands, salt, and intermediate marshes had no discernible relationship between soil carbon and belowground biomass. These results show that different wetland types of Louisiana have distinct variation in soil carbon and soil strength relationships with belowground biomass.

 
Abstract
Biofilm is a collection of microorganisms that adheres to a surface and continues to grow in the presence of nutrients. A clear comparison between the anti-biofilm effect of a DNA phage versus that of an RNA phage needed attention. Furthermore, the effect of nutrient deprivation on an established biofilm is less studied. A study was conducted to compare the biofilm desorption abilities of T4 (a DNA coliphage), and MS2 (an RNA coliphage). Natural biofilms were formed from the microorganisms residing in the recreational water samples. The pure-culture E. coli biofilms were formed from two different strains of E. coli; 11303 E. coli (T4 host), and C3000 E. coli (MS2 host). The established natural biofilms and pure-culture E. coli biofilms were separately treated with Tryptic Soy Broth (TSB), Phosphate Buffered Saline (PBS), T4 phage suspension, and MS2 phage suspension. Natural biofilm desorption was assessed by measuring the optical density. Pure-culture E. coli biofilm desorption was assessed by staining with a 0.1% crystal-violet solution. Results show similar biofilm desorption abilities between T4 and MS2 coliphages. Surprisingly, both natural and pure-culture biofilms were significantly desorbed upon nutrient deprivation. Gene expression was tested of the waaC gene which codes for an enzyme that forms lipopolysaccharide, and the expression of the fimF gene which codes for type I fimbriae minor subunit. While the expressions of both waaC and fimF genes were downregulated upon nutrient deprivation in 11303 E. coli biofilm, these gene expressions were induced upon nutrient deprivation in C3000 E. coli biofilm that was formed in the presence of antibiotics. T4 phage infection resulted in higher waaC and fimF transcripts in 11303 E. coli. Whereas, C3000 E. coli biofilm infected with MS2 phage had reduction in waaC and fimF transcripts. Differential expression of waaC and fimF genes was observed upon phage infection and upon nutrient deprivation. In order to explain this difference in gene expression, the percent change in the number of live cells was compared between phage infection and nutrient deprivation treatments. C3000 and 11303 E. coli biofilms were treated with TSB, PBS, T4 phage suspension, and MS2 phage suspension. An additional treatment of PBS was introduced for C3000 E. coli biofilm grown in the absence of ampicillin and streptomycin. Optical density of the treated biofilms was measured before and after each treatment to determine the percent change. Nutrient deprivation of biofilms resulted in a significantly higher number of live cells within the biofilms as compared to the number of live cells within the biofilms infected with both T4 and MS2 coliphages. These results indicate a presence of distinct biofilm desorption mechanisms upon coliphage treatment and from lack of nutrients.

 
Abstract
Due to a variety of natural and anthropogenic factors, Louisiana has lost approximately a quarter of coastal lands that were present in 1932, thus necessitating restoration activities. A common restoration technique is creating marsh terraces where marsh has been degraded to open water. Terraces provide productive edge habitat and slow land loss by reducing wave energy in surrounding marsh. This study evaluated the influence of marsh terraces on finfish and crustacean assemblages in a brackish marsh east of Golden Meadow, Louisiana. New terraces built in 2022, established terraces built in 2017 and open water habitats were compared. Gee’s® minnow traps, gill nets and a shrimp trawl were used to sample terrace edges, terraces channels and open water. Sampling occurred twice a month from May through October 2022. Finfish and crustaceans were identified to species, counted and measured (mm). Catch per unit effort (CPUE) was calculated as number of individuals collected per unit of effort for each gear type. Mean CPUE (± SE) of minnow trap collected Gulf Killifish Fundulus grandis was greater in established terraces (0.258 ± 0.082) than new terraces (0.009 ± 0.009; F1,22 = 13.43, P = 0.001), but mean CPUE was similar for other finfish and crustacean species (P ≥ 0.05). Gill net mean CPUE was similar for Gafftopsail Catfish Bagre marinus among habitats (F2, 33 = 2.71, P = 0.08). Trawl tow mean CPUE was similar for finfish species (P ≥ 0.05). Blue Crab Callinectes sapidus mean CPUE was higher in established terraces (0.406 ± 0.071), than new terrace (0.111 ± 0.034) and open water habitats (0.117 ± 0.027; F2,33 = 8.40, P < 0.01). Mean CPUE for other crustacean species collected in trawl tows were similar (P ≥ 0.05). Differences in Gulf Killifish relative abundance between established and new terraces may indicate improved edge habitat quality for some marsh-reliant species. Based on trawl data, benthic finfish and crustacean assemblages may not be influenced by marsh terraces. Finfish and crustacean assemblages iv provided insight into possible ecological effects of marsh terraces and how those effects may change over time.

 
Abstract
Southeastern Louisiana is facing extreme rates of coastal wetland loss. The wetland systems occurring in this region provide critical ecosystem functions, benefits, and services for the state and nation. While a myriad of stressors contribute to this loss, one major aspect is the disconnection of annual floodwaters from the Mississippi River to surrounding wetlands. This isolation from river sediment input, in conjunction with natural geologic subsidence, reduces wetland elevations and increases flooding stress. River sediment diversions are large-scale restoration techniques intended to rehabilitate Louisiana’s degraded wetlands by reconnecting the river and surrounding wetlands via controlled, periodic flooding. This process re-connects the surrounding areas with access to subsidies from the river while simulating a natural crevasse splay, building land and stimulating the growth of wetland vegetation. Utilizing such large-scale restoration techniques requires an appropriate knowledge base of vegetation growth and soil biogeochemical responses to altered hydrologic conditions. In this research, sods of three foundational marsh plant species (Spartina patens, Spartina alterniflora, Typha latifolia) were exposed in experimental mesocosms to inundation depths (20 and 40 cm), durations (8 and 16 weeks), nutrient levels (0 and 2 mg L-1 sodium nitrate additive), and salinities (0 and 5 psu) within the range of sediment diversion scenarios. Various indicators of aboveground vegetation growth and soil physicochemical status were measured to investigate likely implications for overall marsh health and sustainability. Monospecific sods of Spartina alterniflora and Typha latifolia displayed a consistent increase in stem densities over time across inundation depth-duration treatments, while Spartina patens displayed a sharp decline in stem densities at 40 cm flooding depths. Additionally, total aboveground biomass was lowest for both Spartina alterniflora and Spartina patens in 40 cm flooding depth treatments. Spartina patens sods displayed a significant loss in elevation with increased flooding stress, whereas Typha latifolia demonstrated a significant gain in elevation. Interestingly, Spartina alterniflora grown in mixture with the other two species displayed a much lower change in stem density compared to monospecific sods. Further, it is notable that Spartina patens in mixture sods also experienced a negative change in stem density at 40 cm-16 week treatments. These findings suggest that Spartina patens and Spartina alterniflora may be outperformed by Typha latifolia in circumstances where flooding stress is coupled with interspecific competition. However, overall results suggest that restoration projects increasing inundation within the limits of the depths and durations examined herein are unlikely to detrimentally impact the aboveground growth responses of Spartina alterniflora or Typha latifolia, but could reduce that of Spartina patens, at least over anticipated river diversion schedules.

 
Abstract
Globally Unionidae is the most abundant freshwater mussel family but is poorly characterized in Louisiana. Historically, populations declined due to overharvest and anthropogenic degradation of habitats. Despite this, Unionidae play a vital role in aquatic ecosystems through filter feeding and substrate stabilization. In Louisiana, distribution and abundance data of mussels is collected by conventional hand sampling methods. However, a more resource-efficient approach, especially for some hard-to-find species, is to collect and sequence environmental DNA (eDNA). Sites were selected opportunistically at bridge crossings and locations accessible by boat in the Sabine (2022, n = 27; 2023, n = 25) and Calcasieu (2022, n = 25; 2023, n = 27) River Basins. All sites were more than 8 km apart. Water samples (~1.5 L) were filtered in the field with encapsulated filters for 600 s. Filters were extracted using the DNeasy® Blood and Tissue Kit (QIAGEN®, Hilden, Germany). DNA extractions were diluted 10-fold with nuclease-free water to reduce PCR inhibition. Order-specific primer assays for cytochrome c oxidase subunit 1 (COI) and NADH dehydrogenase subunit 1 (ND1) were used to amplify DNA fragments. Amplified DNA was purified with MinElute® PCR Purification Kits (QIAGEN®, Hilden, Germany). Purified DNA was again amplified with order-specific COI and ND1 primers ligated with Illumina® (San Diego, California) adapter sequencing regions. Voucher specimens collected from the Calcasieu mainstem were used as positive controls and negative controls were included at each step of the protocol. Environmental DNA fragments were sequenced on the Illumina® MiSeq® platform (San Diego, California). Sequences were collapsed into operational taxonomic units (OTUs) using Qiime2 and then compared to the NCBI BLASTn database for identification. Twenty-three freshwater mussel species were identified using COI, including the proposed federally endangered species Pleurobema riddellii. Five species of greatest conservation need (SGCN) Pleurobema riddellii, Glebula rotundata, Obovaria arkansasensis, Fusconaia askewi, and Strophitus undulatus were detected throughout the Sabine and Calcasieu Rivers Basins. A newly described species, Lampsilis sietmani was detected in the Sabine mainstem which was not previously documented in Louisiana by conventional sampling methods. ND1 detected two OTUs identified as Potamilus purpuratus and Pustulosa pustulosa, but due to low detections, further analysis was not conducted. Further optimization is required to make this marker useful for metabarcoding of Louisiana unionids. Hot spots of freshwater mussel biodiversity were identified and will help managers target restoration projects or future monitoring. This research is the first eDNA project of freshwater mussels conducted in southern Louisiana and informs future research of the difficulties with inhibition and assay failure.

 
Abstract
This project takes place within Terrebonne Parish, Louisiana, an area highly impacted by coastal land loss. The area was historically a cypress swamp that was degraded by exposure to salinities high enough to allow barnacle growth on cypress trees. By the 1990s, when a levee and water control structure were installed as part of the La Cache Marsh Management Project, the area's salinity had already killed most cypress trees, leaving open water with a remnant brackish marsh. In 2019, restoration terraces were constructed to protect the remnant marsh and restore the degraded ecosystem. Here, I present data compiled from my study and results collected prior to my own from February 2019 to August 2023. My characterization of the site includes the documentation of nine large-bodied fish species, eleven amphibian species, 87 bird species, and eight mammal species to illustrate the diversity of species utilizing the site. Additionally, I compared the abundance of crustaceans, small-bodied fish, amphibians, and reptiles associated with the terraces and the remnant marsh to evaluate whether the constructed habitat mimicked the natural habitat. A noticeable decrease in Blue Crab abundance was observed in the study area by 2020 compared to 2019. Sheepshead Minnow was the most abundant species collected, accounting for over 58% of the total small-bodied fish total catch. Although, during some years, there was a difference in the abundance of selected species between the terraces and the marsh by 2023, no significant differences were present. We conclude that the novel design using a tight pattern of terraces led to a habitat that supported a robust assemblage of species resembling that found in the nearby remnant marsh. One unique element of this study site is the occurrence of species rarely seen in freshwater or saltwater habitats but seem to dominate in the intermediate marsh, including Rainwater Killifish, Bayou Killifish, Mississippi Green Watersnake, and Least Bittern.