Agricultural contamination impacts antibiotic resistance gene abundances in river bed sediment temporally.

Kewaunee County, Wisconsin is an agricultural area dominated by concentrated animal feeding operations and manure fertilized cropland. The objective of this study was to characterize chemical and antibiotic resistance gene (ARG) profiles of 20 surface water locations in Kewaunee County to better understand relationships between agricultural contamination and ARG abundance over one year. Surface water (n = 101) and bed sediment (n = 93) were collected from 20 sites during five timepoints between July 2016 and May 2017. Samples were analyzed for six genes (erm(B), tet(W), sul1, qnrA, intI1 and 16S rRNA) and water chemistry and pollution indicators. qnrA, intI1 and sul1 genes in surface water were significantly higher than erm(B) and tet(W); however, no difference was present in sediment samples. Redundancy analysis identified positive correlations of nitrate, Escherichia coli, and coliforms with tet(W) and intI1 genes in sediment and intI1, sul1 and tet(W) genes in water. Temporal patterns of ARG abundance were identified with significantly higher gene abundances found in sediment during Kewaunee County's manure fertilization period; however, surface water patterns were not distinct. Together, these results suggest Kewaunee County sediments serve as a site of accumulation for non-point source agricultural pollution and ARGs on a temporal scale associated with manure fertilization.

Quantitative analysis of the extent of heavy-metal contamination in soils near Picher, Oklahoma, within the Tar Creek Superfund Site.

The Tri-State Mining District of Missouri, Kansas and Oklahoma was the site of large-scale mining operations primarily for lead and zinc until the mid-1950s. Although mining across the area has ceased, high concentrations of heavy metals remain in the region's soil and water systems. The town of Picher, Ottawa County, OK, lies within this district and was included in the Tar Creek Superfund Site by the U.S. Environmental Protection Agency in 1980 due to extensive contamination. To elucidate the extent of heavy-metal contamination, a soil-chemistry survey of the town of Picher was conducted. Samples (n = 111) were collected from mine tailings, locally known as chat, in Picher and along cardinal-direction transects within an 8.05-km radius of the town in August 2015. Samples were analyzed for soil pH, moisture, and metal content. Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) analyses of 20 metals showed high concentrations of lead (>1000 ppm), cadmium (>40 ppm) and zinc (>4000 ppm) throughout the sampled region. Soil moisture content ranged from 0.30 to 35.9%, and pH values ranged from 5.14 to 7.42. MANOVA of metal profiles determined that soils collected from the north transect and chat were significantly different (p < 0.01) than other sampled directions. Lead, cadmium and zinc were correlated with one another. These data show an unequal distribution of contamination surrounding the Picher mining site. Mapping heavy-metal contamination in these soils represents the first step in understanding the distribution of these contaminants at the Picher mining site.

State of remediation and metal toxicity in the Tri-State Mining District, USA.

Mining operations in the Tri-State Mining District of Kansas, Missouri and Oklahoma (TSMD), once one of the major lead and zinc mining areas in the world, had completely ceased by 1970. As mining companies moved out, the land was left with underground tunnels and mine shafts and the surface with abandoned tailings piles, which progressively contaminated groundwater and soil. Despite remedial actions undertaken in the 1980's, areas within the TSMD still contain Cd, Pb, and Zn concentrations exceeding safe levels. Because of the large area and highly dispersed occurrence of wastes, environmental studies generally have been confined either to a stream basin or to a single state. Studies also have differed in their approach and analytical methodologies. An overview of the totality of the TSMD and its present state of contamination is presented here. Data show that metal content in sediments have the following common features: (1) a wide range of Pb and Zn concentrations, up to three orders of magnitude, (2) median values for Cd, Pb and Zn content in sediments and soils were similar among studies, (3) median values for most studies were at or above the guidelines recommended for aquatic habitats, and (4) highest content of Pb and Zn were closely associated with the geographical location of former mining and smelting centers. The above observations imply that mine wastes remain a problem and further remediation is needed. Cost-effective remedial alternatives for this area's geology, climate, and land use, are discussed.

Evidence for placing the false gharial (Tomistoma schlegelii) into the family Gavialidae: inferences from nuclear gene sequences.

The extant crocodylians comprise 23 species divided among three families, Alligatoridae, Crocodylidae, and Gavialidae. Currently, based on morphological data sets, Tomistoma schlegelii (false gharial) is placed within the family Crocodylidae. Molecular data sets consistently support a sister-taxon relationship of T. schlegelii with Gavialis gangeticus (Indian Gharial), which is the sole species in Gavialidae. To elucidate the placement of T. schlegelii within the extant crocodylians, we have sequenced 352bp of the dentin matrix protein 1 (DMP1) nuclear gene in 30 individuals and 424bp of the nuclear gene C-mos in 74 individuals. Molecular analysis of the DMP1 data set indicates that it is highly conserved within the Crocodylia. Of special note is a seven base-pair indel (GTGCTTT) shared by T. schlegelii and G. gangeticus, that is absent in the genus Crocodylus, Osteolaemus, and Mecistops. To date, C-mos is the largest molecular data set analyzed for any crocodylian study including multiple samples from all representatives of the eight extant genera. Analysis of these molecular data sets, both as individual gene sequences and concatenated sequences, support the hypothesis that T. schlegelii should be placed within the family Gavialidae.

Are crocodiles really monophyletic?--Evidence for subdivisions from sequence and morphological data.

Recently, the phylogenetic placement of the African slender snouted crocodile, Crocodylus cataphractus, has come under scrutiny and herein we address this issue using molecular and morphological techniques. Although it is often recognized as being a "basal" form, morphological studies have traditionally placed C. cataphractus within the genus Crocodylus, while molecular studies have suggested that C. cataphractus is very distinct from other Crocodylus. To address the relationship of this species to its congeners we have sequenced portions of two nuclear genes (C-mos 302bp and ODC 294bp), and two mitochondrial genes (ND6-tRNA(glu)-cytB 347bp and control region 457bp). Analyses of these molecular datasets, both as individual gene sequences and as concatenated sequences, support the hypothesis that C. cataphractus is not a member of Crocodylus or Osteolaemus. Examination of 165 morphological characters supports and strengthens our resurrection of an historic genus, Mecistops (Gray 1844) for cataphractus.