Elevating Dissolved Oxygen—Reflections on Developing and Using Long-Term Data

This prospectus took me about as long to generate as my 36—year record of working on the issue of northern Gulf of Mexico (nGOM) oxygen deficiency, or so I felt. There was so much to cover, but I focused on the issue of hypoxia on the Louisiana continental shelf from the early 1980s to present and my participation in the research and outreach. Not that I was ignoring other aspects of my academic research career (e.g., stone crab populations and their differences in physiology and larval development along the nGOM coast; settlement of crab megalopae, especially blue crabs, on artificial substrates and their timing with tidal events; oil and gas pollutant discharges in coastal waters of Louisiana, and as Director of the Coastal Waters Research Consortium (CWC) of the Gulf of Mexico Research Initiative (GoMRI), and marsh infaunal researcher. I must say, however, that the journey through the documentation of low dissolved oxygen on the Louisiana continental shelf, and its linkage to the changes in the Mississippi River nutrient loads to the coastal waters of the nGOM, marked a dominant part of my career. This prospectus follows my research and outreach career from my first journey offshore in an outboard to set stations for the transect off Terrebonne Bay in early summer of 1985 to now

Development of a Real-Time PCR Assay for Detection and Quantification of \u3cem\u3eEscherichia coli\u3c/em\u3e O157:H7 in Apple Juice

Apple cider/juice contaminated with Escherichia coli O157:H7 has been implicated in several foodborne illness outbreaks, but due to the presence of reaction inhibitors, detection by polymerase chain reaction (PCR) is often difficult. The studies presented in this dissertation were conducted to evaluate techniques to improve detection of E. coli O157:H7 in apple juice using a fluorogenic probe-based real-time PCR assay without prior enrichment. Two commercial DNA extraction and purification procedures, GenEluteTM Bacterial Genomic DNA Kit and PrepMan® Ultra Sample Preparation Reagent, were combined with two real-time PCR chemistries, SYBR® Green I dye and TaqMan® probes for potential use in the apple juice assay. After real-time PCR, no significant differences were observed in cycle threshold values (Ct) (p\u3e0.05) among the methods. The PrepMan/TaqMan method was subsequently combined with a real-time PCR assay based on detection of the stx1, stx2, and uidA genes. Apple juice was inoculated individually with nine strains of E. coli O157:H7 (1.0 log CFU/ml to 4.0 log CFU/ml) and plated to verify initial inocula. For particulate removal, apple juice was vacuum filtered twice (Whatman No. 4 and Whatman No. 1), followed by a distilled water wash. Samples were plated again to obtain post-filtration inocula. Filtered juice was centrifuged, pellets were resuspended in 1 ml phosphate buffer, and E. coli O157:H7 cells were concentrated by immunomagnetic separation. PrepMan Ultra was added to the magnetic bead/E. coli O157:H7 complex for DNA extraction. Extracts were combined as appropriate with primers, probe and other reagents, and real-time PCR was performed. Average E. coli O157:H7 inoculum levels of 0.3, 2.2, 3.3 and 4.3 log CFU/ml in apple juice were detected at average Ct values of 41.22, 37.54, 34.69 and 31.81 (stx1); 43.13, 38.74, 35.21 and 32.58 (stx2); and 44.13, 41.54, 37.81 and 34.06 (uidA). Across all E. coli O157:H7 strains, populations as low as 1.6 (44 CFU/ml) (stx1), 1.6 (43 CFU/ml) (stx2), and 1.5 (33 CFU/ml) (uidA) log CFU/ml could be quantified using the cell concentration/real-time PCR assay. However, E. coli O157:H7 was detected on occasion below the quantifiable level at the lowest inoculum level for all strains. This method can be used for rapid detection and quantification (\u3c5 h) of E. coli O157:H7 in apple cider/juice and potentially other foods

Natural History Specimen Collections

The Fish Collection described in this document was transferred in 1992 to the Fish Collection of the University of Texas at Austin in Austin (at that time administratively in the Texas Memorial Museum, but at the time of publication of this digital version of the document it is one (https://biodiversity.utexas.edu/resources/collections/ichthyology) of the Biodiversity Collections in the University's Biodiversity Center (https://biodiversity.utexas.edu/). Thus, the data on the specimens in the Fish Collection described here are now included in the data published to GBIF (https://www.gbif.org/dataset/6080b6cc-1c24-41ff-ad7f-0ebe7b56f311) and other global biodiversity data aggregators by the UT Biodiversity Center's Fish Collection. The same data are also included in the Fishes of Texas Project (http://fishesoftexas.org - Hendrickson, Dean A., and Adam E. Cohen. 2015. “Fishes of Texas Project Database (Version 2.0)” doi:10.17603/C3WC70). Some of the UTMSI Fish Collection specimens remained at the UT Marine Science Insitute on long-term loan from 1992 until sometime in 2017 when the MSI disposed of all remaining specimens (including also Invertebrates). Some were disposed of by a professional HazMat company, but many were apparently taken to the Smithsonian Institution's (USNM) division of Invertebrate Biology. The fate of fish specimens, however, remains unresolved, but the Ichthyology Division at USNM had no knowledge of them at the time this report was archived here. Dean A. Hendrickson, Curator of Ichthyology, UT Austin, May 1, 2019The University of Texas Marine Science Institute, Port Aransas Marine Laboratory, Natural History Collection of Marine Organisms was initiated in the mid-1940's. Since that time specimens have been added from studies in the Gulf of Mexico, associated estuaries, and marine-influenced terrestrial habitats, with emphasis on the Texas and Mexico coasts. These studies were the baseline surveys for this area and have resulted in the collection of valuable marine organisms. The collection now holds approximately 5,000 catalogued specimens including all forms of biota, vertebrates, invertebrates, algae and flowering plants. The collection includes the marine fish and invertebrate specimens of the Texas Parks & Wildlife Department, incorporated into the UTMSI-PAML collection in 1976. This state collection, numbering 3,000, is composed primarily of Texas Gulf coast species of fish and invertebrates, representing baseline surveys conducted by the state fisheries biologists. With this collection are card catalogues by specimen number and phylogenetic order. Other collections incorporated are those from R/V Oregon cruises (U.S. Fish & Wildlife Service, Bureau of Commercial Fisheries, exploratory fishing vessel), H. H. Hildebrand's faunal surveys of the brown and pink shrimp grounds , Whitten et al.'s faunal survey of Texas coast jetties , J. W. Hedgepeth’s specimens collected during numerous faunal surveys, tide trap studies, and vegetation and algal surveys. Noteworthy studies from which specimens have been added to the collection are listed in Table 1. The museum collection is housed in an air-conditioned building in a room specifically designed for this collection. The present facility contains 924 square feet with 1089 square feet of shelf space, which can be trebled to accommodate BLM collections. There are at present 32 1' x 12' shelves, totaling 384 square feet; 194 18" x 12-1/2" shelves, totaling 303 square feet; and 120 11-1/2" x 42" shelves, totaling 402 5 square feet. The collection is a working museum open to the scientific community; specimens are available on loan to members of this community. Specimens may be used by visiting researchers, graduate-level students, professors, and classes. Attached is an invoice form, "Invoice of Specimens" - a standard form used for loan of collection items. The Port Aransas Marine Laboratory is committed to the continuing curation of specimens and will continue to provide the supplies necessary to maintain the natural history specimen collections. The University of Texas Marine Science Institute, Port Aransas Marine Laboratory is willing to incorporate the Bureau of Land Management collection into its collection. Funding is requested from BLM to obtain and incorporate all archived BLM specimens from the S.T.O.C.S. survey into the collection.Integrative Biolog

Coastal Eutrophication near the Mississippi River Delta

CHANGES in delivery of river-borne nutrients such as dissolved phosphate, nitrate and silicate, owing to land-use changes and anthropogenic emissions, are known to result in eutrophication1— enhanced phytoplankton blooms—and more severe hypoxic events2–1 in many enclosed bays and seas. Although similar ecological effects might be expected on continental shelves, the occurrence of such eutrophication has remained unresolved5. Here we present evidence of eutrophication of the continental shelf near the outflow of the Mississippi river, obtained by quantifying biologically bound silica (BSi) in diatom remnants within dated sediment cores. BSi accumulation rates are greatest in water depths of 20 to 50 m within 100 km of the river mouth, and have increased by as much as 100% this century. The increases were substantial by 1980, by which time riverine nitrogen loading had doubled relative to the beginning of the century, even though the silica loading had declined by 50% over the same period. Thus changes in river-borne nutrient loadings can modify coastal food webs and affect the amount and distribution of oxygen in bottom waters on the scale of continental shelves

Linking Landscape And Water Quality In The Mississippi River Basin For 200 Years

Two centuries of land use in the Mississippi River watershed are reflected in the water quality of its streams and in the continental shelf ecosystem receiving its discharge. The most recent influence on nutrient loading-intense and widespread farming and especially fertilizer use-has had a more significant effect on water quality than has land drainage or the conversion of native vegetation to cropland and grazing pastures. The 200-year record of nutrient loading to offshore water is reflected in the paleoreconstructed record of plankton in dated sediments. This record illustrates that the development of fair, sustained management of inland ecosystems is linked to the management of offshore systems. Land use in this fully occupied watershed is under the strong influence of national policies affecting all aspects of the human ecosphere. These policies can be modified for better or worse, but water quality will probably change only gradually because of the strong buffering capacity of the soil ecosystem

Suspended Sediment, C, N, P, and Si Yields from the Mississippi River Basin

The annual loads of C,N,P, silicate, total suspended sediment (mass) and their yields (mass area−1) were estimated for six watersheds of the Mississippi River Basin (MRB) using water quality and water discharge records for 1973 to 1994. The highest load of suspended sediments is from the Missouri watershed (58 mt km2 yr−1), which is also the largest among the six major sub-basins. The Ohio watershed delivers the largest load of water (38%). The Upper Mississippi has the largest total nitrogen load (32%) and yield (1120 kg TN km2 yr−1). The loading of organic carbon, total phosphorus and silicate from the Upper Mississippi and Ohio watersheds are similar and relatively high (range 2.1–2.5, 0.068–0.076, and 0.8–1.1 mt km2 yr−1, respectively). The yields of suspended sediments, total phosphorus, total nitrogen, and silicate from the Lower Mississippi watershed are disproportionately the highest for its area, which is the smallest of all the watersheds and has the weakest monitoring network. The loading from the Red and Arkansas watersheds are of lesser importance than the others for most parameters investigated. The total nitrogen loading to coastal waters increased an additional 150% since the early 1900s, and is now dominated by loads from the Upper Mississippi watershed, rather than the previously dominant Ohio watershed. An analysis of trends for 1973–1994 suggests variability among years, rather than uni-directional change for most variables among 11 key stations. Explanatory relationships were established or confirmed to describe TN and TP loadings in terms of the now largely human-created landscape arising mostly over the last 150 years

The effects of oil on blue crab and periwinkle snail interactions: A mesocosm study

We examined the sub-lethal effect of Macondo oil from the Deepwater Horizon oil spill on predator-prey interactions using blue crabs (Callinectes sapidus) and periwinkle snails (Littoraria irrorata). A 2 x 2 factorial mesocosm design determined the effect of oil (no oil vs. oil) and blue crabs (no blue crab predator vs. one blue crab predator) on periwinkle snail climbing and survival. Sixteen mesocosm tanks were used in the experiment, which were replicated three times. Each tank contained water, sand, and Spartina marsh stems. The sixteen tanks were divided between two, temperature-controlled chambers to separate oil treatments (no oil vs. oil). Oil was buried in the sand to prevent direct coating of mesocosm organisms. Half of the tanks contained only snails, while the other half contained snails and (one) blue crab in each chamber. Snail climbing behavior and survival were documented every 12 h over 96 h. Snails exposed to oil without a blue crab predator survived as well as snails not exposed to oil and no blue crab predator. Oil reduced snail survival in the presence of a blue crab predator. The increase in snail mortality can be attributed to changes in snail climbing behavior. Oil significantly reduced snail climbing height in the presence and absence of a blue crab predator. This change in behavior and subsequent decrease in snail survival could be beneficial for Spartina during recovery after an oil spill. A decrease in snail populations would reduce grazing stress on Spartina. However, field research immediately after an oil spill would be more useful in determining predator-prey interactions and further food web effects

Oxygen Depletion in the Gulf of Mexico Adjacent to the Mississippi River

The seasonal formation of a bottom water layer severely depleted in dissolved oxygen has become a perennial occurrence on the Louisiana continental shelf adjacent to the Mississippi River system. Dramatic changes have occurred in this coastal ecosystem in the last half of the 20th century as the loads of dissolved inorganic nitrogen tripled. There are increases in primary production, shifts in phytoplankton community composition, changes in trophic interactions, and worsening severity of hypoxia. The hypoxic conditions (dissolved oxygen less than 2 mg l-1) cover up to 22,000 km2 of the seabed in mid-summer. Dissolved oxygen concentrations seldom decrease to anoxia, but are often below 1 mg l-1 and down to 0.5 mg l-1. The continental shelf of the northwestern Gulf of Mexico is representative of systems in which nutrient flux to the coastal ocean has resulted in eutrophication and subsequently hypoxia. The Mississippi River influenced continental shelf is similar to systems, such as deep basins and fjords, with regard to biogeochemical processes of oxic versus suboxic conditions in the water column and sediments. However, the suboxic conditions for the Gulf of Mexico are less persistent in time and space due to the dynamic nature of the open continental shelf system. Also, anoxia at the seabed is not as common or long lasting