Development of a Methanogen Marker for Detection of Porcine Fecal Pollution in Surface Waters

The goal of this study was to evaluate methanogen diversity in animal hosts to develop the first swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swine mcrA sequences compared to mcrA sequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed five distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only one mcrA sequence (P23-2) showed specificity for swine and was used for environmental testing. PCR primers for the P23-2 clone mcrA sequence were developed and evaluated for swine-specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%), but did not amplify a product in 47 bacterial and archaeal stock cultures, 477 environmental bacterial isolates, sewage, and water samples from a bovine waste lagoon and polluted creek. Amplification was only observed in 1 sheep out of 260 human and non-swine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pig mcrA sequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10-6 g of wet pig feces in 500 mL of PBS and 10-4 g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker

Contribution of Sediment to High Enterococcus Counts Along the Northern Gulf of Mexico

Enumeration of enterococci (EN) bacteria in water is an USEPA approved indicator of fecal pollution and the possible presence of enteric pathogens. Along the northern Gulf of Mexico, the water is shallow with a high organic and particulate load because of the Mississippi River discharge. Disturbance of coastal sediments during wind/wave action caused either by the weather or human activities may increase bacterial counts as a result of increased EN persistence in the water column and/or resuspension of EN in the sediment. The goals of this project are to determine the relationship between organic content and EN counts in the water and whether bacterial resuspension from the sediment contributes to elevated EN counts. We found that EN counts in the water were correlated with wave conditions at seven sites along the Mississippi Gulf Coast. During calm wave conditions, low bacterial levels (1.0 – 227 CFU/100mL) were observed in the water with higher counts in the sediment; the reverse was observed (10 – 351 CFU/100mL) during rough wave conditions. EN counts were positively correlated with organic content of the sediment. Wave activity to keep EN in suspension was apparently critical for high counts. EN counts decreased by 50% in 4 hr from 38 to 17 CFU/100mL in the absence of resuspension and decreased to 1 CFU/100mL after 48 hr. EN in the sediment are not stationary as genetic fingerprinting using REP-PCR showed low persistence of specific isolates over time. Jackknife analysis revealed low similarity among EN isolates from the water and sediment collected on the same day and site during calm wave conditions. This shows that EN are not persisting for long periods in the same area but instead are resuspended and redistributed along the coast. Results from this study provide evidence that high organic content and resuspension of isolates from the sediment during periods of strong wave action contribute to high EN counts. Current research on the survival of EN in estuarine habitats will provide insight on the balance between environmental persistence and fecal pollution in causing high EN counts along beaches in the northern Gulf of Mexico

Early-Cenomanian Terrestrial Facies and Paleoclimate Records of the Lower Tuscaloosa Formation, Southwestern Mississippi

Sphaerosiderite oxygen isotope values from the Early Cenomanian Lower Tuscaloosa Formation, or LTF, extend a mid-Cretaceous meteoric delta O-18 latitudinal gradient 9 degrees south to25 degrees N paleolatitude, and contribute to a better understanding of the hydrologic cycle in North America during a greenhouse period in Earth history. Sphaerosiderites have been used to reconstruct paleolatitudinal trends in meteoric O-18 values throughout western North America, and the O-18 values have been used in a stable isotope mass balance model to produce quantitative estimates of mid-Cretaceous precipitation rates and latent heat flux values. The LTF meteoric O-18 values help constrain the critical subtropical values on the coastal plain bordering Tethys and the southeastern coast of the Western Interior Seaway. The LTF, an important subsurface petroleum unit (2800-4000 m depths) in southern Mississippi, contains amalgamated pedogenicallymodified, sphaerosiderite-bearing mudstones and sandstones. Cored intervals of the Early-Cenomanian Stringer Sandstone Member of the Lower Tuscaloosa Formation (LTF) of Southwestern Misississippi are characterized by 6 lithofacies units. The descriptive lithofacies units include: (1) thickly-bedded sandstones; (2) thinly bedded sandstones; (3) carbonaceous mudstones and siltstones; (4) red-mottled rnudstones; (5) purple and yellow mottled mudstones; and (6) flaser and lenticular bedded carbonaceous muddy sandstones. The sphaerosiderites are most commonly observed in gleyed domains of the red-mottled mudstones. These mudstones were clays, and silty clay loam soils, and are characterized by prominent red mottles in a gleyed matrix with an abundance of translocated clays, pedogenic slickensides, carbonaceous debris, and root traces. The sphaerosiderites yield delta O-18 vs. delta C-18 values, meteoric sphaerosiderite lines (MSLs), that may be used as a proxy for paleoprecipitation delta O-18 values. The MSL (delta O-18) values range from -3.31% to - 5.22% (VPDB). Estimated meteoric water values for the LTF have an average value of -4.69 % VSMOW

Clay Coatings From a Modem Soil Chronosequence: A Tool for Estimating the Relative Age of Well-Drained Paleosols

Blue light optically stimulated luminescence (OSL) dates obtained from upland and terrace soil profiles in southeastern Mississippi have been used to generate a model for illuvial clay accumulation in deeply weathered, subtropical soils (e.g. Ultisols). The illuvial clays developed in upland vs. alluvial terrace soils of southeastern Mississippi are distinct in terms of thickness and total volume of translocated clay. The coatings in the Mississippi soils are also an analogue for clay coatings observed in mid-Cretaceous paleosols of North America. Many of the Cretaceous paleosols had a polygenefic history. The relative age of the well-drained phase of pedogenic development, characterized by illuvial clay accumulations, may be estimated using the model generated from the Mississippi soils. As many of the mid-Cretaceous palcosols mark unconformities, it would be beneficial to estimate the duration of the hiatuses. Three geomorphic surfaces characterize the landscape of southeastern Mississippi: uplands, stream-cut terraces, and modem alluvium. The present floodplain, has poorly developed soils, and lacks illuvial accumulations. Soils developing in the uplands have abundant and prominent illuvial clay coatings up to 2 mm thick, while the terraces have minor clay coatings less than I mm thick. (c) 2007 Elsevier B.V All rights reserved

\u3ci\u3eMethanobrevibacter ruminantium\u3c/i\u3e as an Indicator of Domesticated-Ruminant Fecal Pollution in Surface Waters

A PCR-based assay (Mrnif) targeting the nifH gene of Methanobrevibacter ruminantium was developed to detect fecal pollution from domesticated ruminants in environmental water samples. The assay produced the expected amplification product only when the reaction mixture contained DNA extracted from M. ruminantium culture, bovine (80%), sheep (100%), and goat (75%) feces, and water samples from a bovine waste lagoon (100%) and a creek contaminated with bovine lagoon waste (100%). The assay appears to be specific and sensitive and can distinguish between domesticated- and nondomesticated-ruminant fecal pollution in environmental samples

Development of a Swine-Specific Fecal Pollution Marker Based on Host Differences in Methanogen mcrA Genes▿

The goal of this study was to evaluate methanogen diversity in animal hosts to develop a swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swine mcrA sequences compared to mcrA sequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed four distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only one mcrA sequence (P23-2) showed specificity for swine and therefore was used for environmental testing. PCR primers for the P23-2 clone mcrA sequence were developed and evaluated for swine specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%) but did not amplify a product in 47 bacterial and archaeal stock cultures and 477 environmental bacterial isolates and sewage and water samples from a bovine waste lagoon and a polluted creek. Amplification was observed in only one sheep sample out of 260 human and nonswine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pig mcrA sequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10−6 g of wet pig feces in 500 ml of phosphate-buffered saline and 10−4 g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker

Development of a Swine-Specific Fecal Pollution Marker Based on Host Differences in Methanogen \u3ci\u3emcrA\u3c/i\u3e Genes

The goal of this study was to evaluate methanogen diversity in animal hosts to develop a swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swine mcrA sequences compared to mcrA sequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed four distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only one mcrA sequence (P23-2) showed specificity for swine and therefore was used for environmental testing. PCR primers for the P23-2 clone mcrA sequence were developed and evaluated for swine specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%) but did not amplify a product in 47 bacterial and archaeal stock cultures and 477 environmental bacterial isolates and sewage and water samples from a bovine waste lagoon and a polluted creek. Amplification was observed in only one sheep sample out of 260 human and nonswine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pig mcrA sequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10−6 g of wet pig feces in 500 ml of phosphate-buffered saline and 10−4 g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker

Evolution of a Salt Diapir Within the Mississippi Salt Basin, USA: Interaction of Salt Migration and Sediment Deposition

Utilizing proprietary 3-D seismic data, the growth history of a shallow piercement diapir within the Mississippi Salt Basin has been interpreted as five distinct phases of salt mobilization: (1) Initial loading by Late Jurassic sedimentation mobilized tabular salt, forming a northeast-southwest-trending ridge flanked by discontinuous primary salt welds. (2) Early Cretaceous sedimentation restricted salt withdrawal to dimensions defined by primary salt weld development parallel to ridge orientation. Dominant salt withdrawal was from the northeast. Thickening of the interval was accompanied by development of a linked ridge-salt stock system. (3) Late Cretaceous loading of the ridge, in combination with burial compaction and subsidence along the flanks of the salt stock, led to the collapse of deep-seated feeders, development of bulb-shaped morphology, and a decrease in salt sourced from the northeast portion of the ridge, along with an increase in salt sourced from the southwest. (4) Vertical migration driven by subsidence and burial compaction along the flanks of the diapir, and a shift from rapid deposition of thick clastic overburden to slower overburden deposition of the Selma Chalk and Midway Shale, exposed the salt stock at the sea floor in a passive state. (5) Deposition of thick Wilcox siliclastics buried the diapir, causing a rejuvenation of vertical salt migration and continuation of drag fold development along diapir flanks during shallow piercement. We conclude that phases of salt mobilization correlate with phases of depositional loading, making it possible to develop a more detailed evolutionary history of salt structures in interior salt basins than proposed in the past

High Latitude Meteoric δ\u3csup\u3e18\u3c/sup\u3eO Compositions: Paleosol Siderite in the Middle Cretaceous Nanushuk Formation, North Slope, Alaska

Siderite-bearing pedogenic horizons of the Nanushuk Formation of the North Slope, Alaska, provide a critical high paleolatitude oxygen isotopic proxy record of paleoprecipitation, supplying important empirical data needed for paleoclimatic reconstructions and models of “greenhouse- world” precipitation rates. Siderite δ18O values were determined from four paleosol horizons in the National Petroleum Reserve Alaska (NPR-A) Grandstand # 1 Core, and the values range between −17.6‰ and −14.3‰ Peedee belemnite (PDB) with standard deviations generally less than 0.6‰ within individual horizons. The δ13C values are much more variable, ranging from −4.6‰ to +10.8‰ PDB. A covariant δ18O versus δ13C trend in one horizon probably resulted from mixing between modified marine and meteoric phreatic fluids during siderite precipitation. Groundwater values calculated from siderite oxygen isotopic values and paleobotanical temperature estimates range from −23.0‰ to −19.5‰ standard mean ocean water (SMOW). Minor element analyses show that the siderites are impure, having enrichments in Ca, Mg, Mn, and Sr. Minor element substitutions and Mg/Fe and Mg/(Ca + Mg) ratios also suggest the influence of marine fluids upon siderite precipitation. The pedogenic horizons are characterized by gleyed colors, rare root traces, abundant siderite, abundant organic matter, rare clay and silty clay coatings and infillings, some preservation of primary sedimentary stratification, and a lack of ferruginous oxides and mottles. The pedogenic features suggest that these were poorly drained, reducing, hydromorphic soils that developed in coal-bearing delta plain facies and are similar to modern Inceptisols. Model-derived estimates of precipitation rates for the Late Albian of the North Slope, Alaska (485–626 mm/yr), are consistent with precipitation rates necessary to maintain modern peat-forming environments. This information reinforces the mutual consistency between empirical paleotemperature estimates and isotope mass balance models of the hydrologic cycle and can be used in future global circulation modeling (GCM) experiments of “greenhouse- world” climates to constrain high latitude precipitation rates in simulations of ancient worlds with decreased equator-to-pole temperature gradients

Reconstructing a Mid-Cretaceous Landscape From Paleosols In Western Canada

The Albian Stage of the mid-Cretaceous was a time of equable climate conditions with high sea levels and broad shallow epeiric seas that may have had a moderating affect on continental climates. A Late Albian landscape surface that developed during a regression and subsequent sea-level rise in the Western Canada Foreland Basin is reconstructed on the basis of correlation of paleosols penetrated by cores through the Paddy Member of the Peace River Formation. Reconstruction of this landscape refines chronostratigraphic relationships and will benefit future paleoclimatological studies utilizing continental sphaerosiderite proxy records. The paleosols developed in estuarine sandstones and mudstones, and they exhibit evidence of a polygenetic history. Upon initial exposure and pedogenesis, the Paddy Member developed deeply weathered, well-drained cumulative soil profiles. Later stages of pedogenesis were characterized, by hydromorphic soil conditions. The stages of soil development interpreted for the Paddy Member correlate with inferred stages of pedogenic development in timeequivalent formations located both basinward and downslope (upper Viking Formation), and landward and upslope (Boulder Creek Formation). On the basis of the genetic similarity among paleosols in these three correlative formations, the paleosols are interpreted as having formed along a single, continuous landscape surface. Results of this study indicate that the catena concept of pedogenesis along sloping landscapes is applicable to ancient successions. Sphaerosiderites; in the Paddy Member paleosols are used to provide proxy values for meteoric delta(18)O values at 52 degrees N paleolatitude in the Cretaceous Western Interior Basin. The meteoric delta(18)O values are used to refine existing interpretations about the mid-Cretaceous paleolatitudinal gradient in meteoric delta(18)O values, and the mid-Cretaceous hydrologic cycle