Gene expression in the olfactory epithelia of parasitic and reproductive adult sea lampreys
ABSTRACT: To determine gene expression differences in the olfactory epithelium of sea lamprey between sequential yet behaviorally distinct adult life history stages 2 samples: parasitic adults removed from fish in northern Lake Huron and Lake Michigan in February and March, and reproductive adults collected from Lake Huron and Lake Michigan tributaries in June
Project description:To determine gene expression differences in the olfactory epithelium of sea lamprey between sequential yet behaviorally distinct adult life history stages Overall design: 2 samples: parasitic adults removed from fish in northern Lake Huron and Lake Michigan in February and March, and reproductive adults collected from Lake Huron and Lake Michigan tributaries in June
Project description:Maintenance of genetic and phenotypic diversity is widely recognized as an important conservation priority, yet managers often lack basic information about spatial patterns of population structure and its relationship with habitat heterogeneity and species movement within it. To address this knowledge gap, we focused on the economically and ecologically prominent yellow perch (Perca flavescens). In the Lake Michigan basin, yellow perch reside in nearshore Lake Michigan, including drowned river mouths (DRMs)-protected, lake-like habitats that link tributaries to Lake Michigan. The goal of this study was to examine the extent that population structure is associated with Great Lakes connected habitats (i.e., DRMs) in a mobile fish species using yellow perch as a model. Specifically, we tested whether DRMs and eastern Lake Michigan constitute distinct genetic stocks of yellow perch, and if so, whether those stocks migrate between the two connected habitats throughout the year. To do so, we genotyped yellow perch at 14 microsatellite loci collected from 10 DRMs in both deep and littoral habitats during spring, summer, and autumn and two nearshore sites in Lake Michigan (spring and autumn) during 2015-2016 and supplemented our sampling with fish collected in 2013. We found that yellow perch from littoral-DRM habitats were genetically distinct from fish captured in nearshore Lake Michigan. Our data also suggested that Lake Michigan yellow perch likely use deep-DRM habitats during autumn. Further, we found genetic structuring among DRMs. These patterns support hypotheses of fishery managers that yellow perch seasonally migrate to and from Lake Michigan, yet, interestingly, these fish do not appear to interbreed with littoral fish despite occupying the same DRM. We recommend that fisheries managers account for this complex population structure and movement when setting fishing regulations and assessing the effects of harvest in Lake Michigan.
Project description:Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.
Project description:The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.Four phages were extracted from Lake Michigan on the same bacterial host, exhibiting similar morphological characteristics as shown under transmission electron microscopy. Growth characteristics of the phages were unique to each isolate. Each phage demonstrated a host-range spanning several phyla of bacteria - to date, such a broad host-range is yet to be reported. Genomic data reveals genomes of a similar size, and close similarities between the Lake Michigan phages and the Pseudomonas phage PB1, however, the majority of annotated genes present were ORFans and little insight was offered into mechanisms for host-range.The phages isolated from Lake Michigan are capable of infecting several bacterial phyla, and demonstrate varied phenotypic characteristics despite similarities in host preference, and at the genomic level. We propose that such a broad host-range is likely related to the oligotrophic nature of Lake Michigan, and the competitive benefit that this characteristic may lend to phages in nature.
Project description:BACKGROUND:Most Lyme disease cases in the Midwestern United States are reported in Minnesota and Wisconsin. In recent years, however, a widening geographic extent of Lyme disease has been noted with evidence of expansion eastwards into Michigan and neighboring states with historically low incidence rates. METHODS:We collected confirmed and probable cases of Lyme disease from 2000 through 2014 from the Michigan Department of Health and Human Services, entering them in a geographic information system. We performed spatial focal cluster analyses to characterize Lyme disease expansion. We compared the distribution of human cases with recent Ixodes scapularis tick distribution studies. RESULTS:Lyme disease cases in both the Upper and Lower Peninsulas of Michigan expanded more than 5-fold over the study period. Although increases were seen throughout the Upper Peninsula, the Lower Peninsula particularly expanded along the Indiana border north along the eastern shore of Lake Michigan. Human cases corresponded to a simultaneous expansion in established I scapularis tick populations. CONCLUSIONS:The geographic distribution of Lyme disease cases significantly expanded in Michigan between 2000 and 2014, particularly northward along the Lake Michigan shore. If such dynamic trends continue, Michigan-and possibly neighboring areas of Indiana, Ohio, and Ontario, Canada-can expect a continued increase in Lyme disease cases.
Project description:PAHs in the Great Lakes basin are of concern due to their toxicity and persistence in bottom sediments. Their nitro derivatives, nitro-PAHs (NPAHs), which can have stronger carcinogenic and mutagenic activity than parent PAHs, may follow similar transport routes and also are accumulated in sediments. Limited information exists regarding the current distribution, trends and loadings of these compounds, especially NPAHs, in Lake Michigan sediments. This study characterizes PAHs, NPAHs, and biomarkers steranes and hopanes in surface sediments collected at 24 offshore sites in southern Lake Michigan. The ?PAH14 (sum of 14 compounds) ranged from 213 to 1,291 ng/g dry weight (dw) across the sites, levels that are 2 to 10 times lower than those reported 20 to 30 years earlier. Compared to consensus-based sediment quality guidelines, PAH concentrations suggest very low risk to benthic organisms. The ?NPAH5 concentration ranged from 2.9 to 18.6 ng/g dw, and included carcinogenic compounds 1-nitropyrene and 6-nitrochrysene. ?Sterane6 and ?Hopane5 concentrations ranged from 6.2 to 36 and 98 to 355 ng/g dw, respectively. Based on these concentrations, Lake Michigan is approximately receiving 11, 0.16, 0.25 and 3.6 metrictons per year (t/yr) of ?PAH14, ?NPAH5, ?Sterane6 and ?Hopane5, respectively. Maps of OC-adjusted concentrations display that concentrations decline with increasing off-shore distance. The major sources of PAHs and NPAHs are pyrogenic in nature, based on diagnostic ratios. Using chemical mass balance models, sources were apportioned to emissions from diesel engines (56 ± 18%), coal power plants (27 ± 14%), coal-tar pavement sealants (16 ± 11%), and coke ovens (7 ± 12%). The biomarkers identify a combination of petrogenic and biogenic sources, with the southern end of the lake more impacted by petroleum. This first report of NPAH levels in sediments of Lake Michigan reveals several carcinogenic compounds at modest concentrations, and a need for further work to assess potential risks to aquatic organisms.
Project description:Lake Michigan surface waters impacted by fecal pollution were assessed to determine the occurrence of genetic markers for Bacteroides and Escherichia coli. Initial experiments with sewage treatment plant influent demonstrated that total Bacteroides spp. could be detected by PCR in a 25- to 125-fold-higher dilution series than E. coli and human-specific Bacteroides spp., which were both found in similar dilution ranges. The limit of detection for the human-specific genetic marker ranged from 0.2 CFU/100 ml to 82 CFU/100 ml culturable E. coli for four wastewater treatment plants in urban and rural areas. The spatial and temporal distributions of these markers were assessed following major rain events that introduced urban storm water, agricultural runoff, and sewage overflows into Lake Michigan. Bacteroides spp. were detected in all of these samples by PCR, including those with <1 CFU/100 ml E. coli. Human-specific Bacteroides spp. were detected as far as 2 km into Lake Michigan during sewage overflow events, with variable detection 1 to 9 days postoverflow, whereas the cow-specific Bacteroides spp. were detected in only highly contaminated samples near the river outflow. Lake Michigan beaches were also assessed throughout the summer season for the same markers. Bacteroides spp. were detected in all beach samples, including 28 of the 74 samples that did not exceed 235 CFU/100 ml of E. coli. Human-specific Bacteroides spp. were detected at three of the seven beaches; one of the sites demonstrating positive results was sampled during a reported sewage overflow, but E. coli levels were below 235 CFU/100 ml. This study demonstrates the usefulness of non-culture-based microbial-source tracking approaches and the prevalence of these genetic markers in the Great Lakes, including freshwater coastal beaches.
Project description:The U.S. EPA's Great Lakes National Program Office (GLNPO) annual water quality survey (WQS) collects data at a relatively small number of stations in each lake. The survey was designed to measure conditions in the open-water regions of the lakes where an assumption of spatial homogeneity was thought likely to be met and the measured variables could be characterized by simple statistics. Here we use satellite observations to assess how well statistics based on samples collected in the GLNPO sampling network represent the lake-wide values of two variables, surface chlorophyll concentration and Secchi depth. We find strong linear relationships between the mean values calculated from the samples and the corresponding averages based on the subsets of the full satellite images. Although overall the means of the values from the sample locations agree well with means calculated from most of the non-coastal regions of the lakes, in terms of water depth, the GLNPO station averages best represent the regions of Lake Huron deeper than 30 m, of Lakes Michigan and Superior deeper than 90 m, and of Lake Ontario deeper than 60 m. When the lake regions are defined by distance offshore rather than by depth, the GLNPO station chlorophyll means in Lakes Huron, Ontario, and Superior are closest to the means for the area of the lakes > 10 km offshore. In Lake Michigan the closest correspondence is with the > 20 km offshore region. On a whole-lake basis in Lake Erie the GLNPO station chlorophyll averages are closest to the average calculated from the entire lake.
Project description:We have quantified the release of polychlorinated biphenyls (PCBs) from Indiana Harbor and Ship Canal (IHSC) to Lake Michigan and the atmosphere. Navigational dredging is planned for this system, and there is concern that dredging will result in releases of PCBs. We have analyzed greater than 158 PCBs in surficial sediment, water, suspended particles, and air. We predicted the release of PCBs from sediments to water and from water to air. To quantify the level of confidence in our calculations, we used a Monte Carlo simulation for each congener flux. We determined that 4 +/- 0.05 kg of summation operatorPCBs were released from the sediment to the water and 7 +/- 0.1 kg of summation operatorPCBs were volatilized from the water to the air annually. We measured input from the upstream regions of the canal system of 45.0 kg yr(-1) and export to Lake Michigan of 43.9 kg yr(-1). The summation operatorPCBs mass balance accounts for nearly all the PCB inputs and losses to the navigational regions. The congener profiles in sediment, water, and air support our determination that the contaminated sediment is a major source of PCBs into the water and air above it. We have shown that the system is currently a significant source of PCBs to the air and to Lake Michigan, even under quiescent conditions.
Project description:The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7-41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.