Geology ReportsSearch

SEARCH · Geology Reports

Results for “Biomarkers”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

Individual variability in esterase activity and CYP1A levels in Chinook salmon (Oncorhynchus tshawytscha) exposed to esfenvalerate and chlorpyrifos

Acetylcholinesterase (AChE) activity has traditionally been monitored as a biomarker of organophosphate (OP) and/or carbamate exposure. However, AChE activity may not be the most sensitive endpoint for these agrochemicals, because OPs can cause adverse physiological effects at concentrations that do not affect AChE activity. Carboxylesterases are a related family of enzymes that have higher affinity than AChE for some OPs and carbamates and may be more sensitive indicators of environmental exposure to these pesticides. In this study, carboxylesterase and AChE activity, cytochrome P4501A (CYP1A) protein levels, and mortality were measured in individual juvenile Chinook salmon (Oncorhynchus tshawytscha) following exposure to an OP (chlorpyrifos) and a pyrethroid (esfenvalerate). As expected, high doses of chlorpyrifos and esfenvalerate were acutely toxic, with nominal concentrations (100 and 1 ??g/l, respectively) causing 100% mortality within 96 h. Exposure to chlorpyrifos at a high dose (7.3 ??g/l), but not a low dose (1.2 ??g/l), significantly inhibited AChE activity in both brain and muscle tissue (85% and 92% inhibition, respectively), while esfenvalerate exposure had no effect. In contrast, liver carboxylesterase activity was significantly inhibited at both the low and high chlorpyrifos dose exposure (56% and 79% inhibition, respectively), while esfenvalerate exposure still had little effect. The inhibition of carboxylesterase activity at levels of chlorpyrifos that did not affect AChE activity suggests that some salmon carboxylesterase isozymes may be more sensitive than AChE to inhibition by OPs. CYP1A protein levels were ???30% suppressed by chlorpyrifos exposure at the high dose, but esfenvalerate had no effect. Three teleost species, Chinook salmon, medaka (Oryzias latipes) and Sacramento splittail (Pogonichthys macrolepidotus), were examined for their ability to hydrolyze a series of pyrethroid surrogate substrates and in all cases hydrolysis activity was undetectable. Together these data suggest that (1) carboxylesterase activity inhibition may be a more sensitive biomarker for OP exposure than AChE activity, (2) neither AChE nor carboxylesterase activity are biomarkers for pyrethroid exposure, (3) CYP1A protein is not a sensitive marker for these agrochemicals and (4) slow hydrolysis rates may be partly responsible for acute pyrethroid toxicity in fish. ?? 2005 Elsevier B.V. All rights reserved.

Aquatic Toxicology

Molecular indicators of methane metabolisms at cold seeps along the United States Atlantic margin

A lipid biomarker study was undertaken to determine the microbial composition and variability in authigenic carbonates and associated soft bottom habitats from the Norfolk and the Baltimore Canyon seep fields along the US mid-Atlantic margin. Results from this study capture a distinct molecular signal from methane oxidizing archaea, including archaeol (I), sn-2-hydroxyarchaeol, pentamethylicosane (PMI), and crocetane. These consortia of methane-oxidizing Archaea have been identified as carrying out anaerobic oxidation of methane (AOM), thereby favoring the precipitation of methane derived authigneic carbonates. The carbon isotope (δ13C) values of AOM-related lipids were strongly depleted in 13C, (i.e., archaeol: -91.64 ‰, sn-2-hydroxyarchaeol: -129.18 ‰, pentamethylicosane (PMI); -131.36 ‰, and crocetane: -70.94 ‰), confirming the dominance of methane as the dominant carbon source for the Archaea during AOM fractionation. The presence of terminally branched fatty acids such as the antesio- and iso-C15:0 components, diagnostic of sulfate-reducing bacteria (SRB), and their depleted δ13C signature (-107.6 ‰), supports syntrophy of SRB with methane-oxidizing archaea. While lipid biomarker profiles of authigenic carbonates biomarker are similar to those found in the seep sediment, suggesting a similar microbial assemblage within the seep-microbiome, a range in lipid composition, distribution, and isotopic signature between seep sites and matrix type suggests AOM is performed by multiple archaeal sources, instead of a single archaeal species.

Atlantic margin

Chemical contamination of the Rybinsk Reservoir, northwest Russia: Relationship between liver polychlorinated biphenyls (PCB) content and health indicators in bream (Abramis brama)

The Rybinsk Reservoir (Russia) is the largest artificial waterbody in Europe (4550 km 2 ) and provides drinking water for population of the cities located along the coast line. Industrialization in Cherepovets at the northeastern portion of the reservoir, including one of the largest metallurgical facilities in Europe, has resulted in chemical contamination of the reservoir. The extent of polychlorinated biphenyls (PCB) contamination in bream liver, a common fish species, taken from six locations in the Rybinsk Reservoir and Volga River, and biochemical and morphometric biomarkers of fish health were investigated. Liver PCB concentrations ranged from non-detected to 3.4 μg/g wet wt of liver, with the greatest concentrations found in fish taken near the industrialized area in Sheksna Reach of Rybinsk Reservoir. The source of the bream contamination is the PCB pollution of bottom organisms and sediments conditioned with industrialization facilities of Cherepovets. The patterns of the PCB congeners in the livers of bream taken near Cherepovets were similar at all of the stations that were sampled around the reservoir and Volga River. Among the common fish health biomarkers used only liver total ChE activity and liver-somatic index in bream near Cherepovets can reflect environmental pollution. Other morphometric (FCF, Clark’s condition factors, and spleen-somatic index) and biochemical (protein content and acetylcholinesterase activity in the brain) biomarkers related with fish health varied among locations, but were not correlated to the concentrations of PCBs in the bream livers.

Rybinsk Reservoir

Differentiating persistent and intermittent euxinia from the molecular derivatives of green sulfur bacteria carotenoids

Green sulfur bacteria biomarkers that indicate euxinia within the photic zone sometimes co-occur with evidence of contradictory depositional redox conditions, such as oxygen-requiring fossils or bioturbation. Intermittent euxinia may explain this apparent contradiction, and recent studies of modern environments show that green sulfur bacteria dwell in transiently euxinic settings. As a result, new approaches are needed to distinguish green sulfur bacteria biomarkers indicative of persistent versus intermittent euxina in ancient sedimentary samples, which this study addresses by investigating how the distribution of isorenieratene derivatives relates to depositional redox conditions. To accomplish this objective, this study focuses on two drill cores through the Upper Cretaceous Mowry Shale and the Eagle Ford Group. These drill cores are comparably thermally immature according to vitrinite reflectance data, and these formations in these cores capture a spectrum of depositional redox conditions according to multiple organic and inorganic proxies, including newly acquired iron speciation and kerogen organic sulfur data. The results presented here reveal that higher molecular weight diagenetic products of isorenieratene are preferentially preserved under persistent euxinia compared to intermittently euxinic intervals that contain isorenieratene derivatives that are shifted to lower molecular weights. Further, the total inventory of aromatic carotenoid diagenetic products contains features that can be used to identify green sulfur bacteria biomarkers from reworked petrogenic sources. Accordingly, the diagenetic fate of isorenieratene and the distribution of its diagenetic products distinguish persistent versus intermittent euxinia, which can be used to sharpen our evaluation of euxinia in the geologic record.

Geochemica et Cosmochimica Acta

Geochemical advances in Arctic Alaska oil typing - North Slope oil correlation and charge history

The Arctic Alaska petroleum province is geologically and geochemically complex. Mixed hydrocarbon charge from multiple source rocks and/or levels of thermal maturity is common within an individual oil pool. Biomarker and chemometric statistical analyses were used to correlate twenty-nine oils to five oil families derived from: (1) Triassic Shublik Formation (calcareous organofacies), (2) Triassic Shublik Formation (shaly organofacies), (3) Jurassic Kingak Shale, (4) Cretaceous shale (pebble shale unit and Hue Shale), and (5) Paleogene shale (Canning Formation). Age-diagnostic and source-related oil biomarker parameters establish clear genetic relationships between the normal oil-window components and their putative source designations. However, application of diamondoid analyses reveals mixed-oil accumulations with postmature charge contributions (diamondoid-rich and biomarker-poor) in many oils. Most sampled reservoirs contain a predominant charge derived from a single oil-window source plus a minor contribution from one or more higher maturity source(s). Variations in source organofacies also are recognized in the Shublik, Kingak, and Cretaceous oil families. In some cases, oils from multiple pools within a single field display relatively homogeneous geochemical profiles, suggesting a common source and migration pathway. For example, oil from the significant Pikka discovery is inferred to originate mainly from the calcareous Shublik Formation. In other cases, variability among oils from multiple pools within a single field (e.g., Milne Point, Colville River, and Northstar) likely indicates a more complex source, migration, and charge history. Results may be useful for anticipating the composition of oil charge in stratigraphic traps with low-permeability sandstone reservoirs, where oil gravity and other chemical parameters may influence economic viability.

Alaska

Historical changes in organic matter input to the muddy sediments along the Zhejiang-Fujian Coast, China over the past 160 years

The burial of sedimentary organic matter (SOM) in the large river-influenced estuarine-coastal regions is affected by hydrodynamic sorting, diagenesis and human activities. Typically, the inner shelf region of the East China Sea is a major carbon sink of the Yangtze River-derived fine-grained sediments. Most of the previous work concentrated on the studies of surface sediments or used a single-proxy in this region. In this study, two cores from the Zhejiang-Fujian Coast were analyzed using bulk (TOC, TN and δ 13 C TOC ) and molecular biomarker ( n -alkane, brassicasterol, dinosterol and glycerol dialkyl glycerol tetraether lipids) techniques to clarify the sources, spatiotemporal distribution and fate of SOM in the Yangtze River Estuary and adjacent shelf. Results from this study indicated that the effects of diagenesis and diffusion on different sedimentary biomarkers resulted in overestimation of the relative contribution of terrestrial organic matter (%OM terr ), compared with those based on δ 13 C TOC . The amounts of terrestrial plant organic matter (OM plant ) and%OM terr in sediments decreased offshore. In contrast, the amounts of marine organic matter (OM marine ) increased offshore, but closer to the Yangtze River mouth, the amounts of soil organic matter (OM soil ) increased. Moreover, the amounts of TOC, OM plant and OM marine biomarkers increased, but OM soil and%OM terr decreased over time in recent decades. Our study suggests that spatial organic matter distribution patterns in marine shelf sediments were controlled primarily by hydrodynamic sorting and nutrient concentrations, and temporally diverse patterns were controlled predominantly by anthropogenic influence (e.g., dam construction and soil conservation, reclamation and agricultural plantations, anthropogenic nutrient input, dust storms, eutrophication, etc) and climate events (e.g., interdecadal climatic jump and heavy rain events) in the geological period.

Zhejiang-Fujian Coast

Long-term assessment of relationships between changing environmental conditions and the physiology of southern Beaufort Sea polar bears (Ursus maritimus)

Climate change is influencing polar bear ( Ursus maritimus ) habitat, diet, and behavior but the effects of these changes on their physiology is not well understood. Blood-based biomarkers are used to assess the physiologic health of individuals but their usefulness for evaluating population health, especially as it relates to changing environmental conditions, has rarely been explored. We describe links between environmental conditions and physiologic functions of southern Beaufort Sea polar bears using data from blood samples collected from 1984 to 2018, a period marked by extensive environmental change. We evaluated associations between 13 physiologic biomarkers and circumpolar (Arctic oscillation index) and regional (wind patterns and ice-free days) environmental metrics and seasonal and demographic co-variates (age, sex, season, and year) known to affect polar bear ecology. We observed signs of dysregulation of water balance in polar bears following years with a lower annual Arctic oscillation index. In addition, liver enzyme values increased over time, which is suggestive of potential hepatocyte damage as the Arctic has warmed. Biomarkers of immune function increased with regional-scale wind patterns and the number of ice-free days over the Beaufort Sea continental shelf and were lower in years with a lower winter Arctic oscillation index, suggesting an increased allocation of energetic resources for immune processes under these conditions. We propose that the variation in polar bear immune and metabolic function is likely indicative of physiologic plasticity, a response that allows polar bears to remain in homeostasis even as they experience changes in nutrition and habitat in response to changing environments.

Alaska

Bioindicators of contaminant exposure and effect in aquatic and terrestrial monitoring

Bioindicators of contaminant exposure presently used in environmental monitoring arc discussed. Some have been extensively field-validated and arc already in routine application. Included are (1) inhibition of brain or blood cholinesterase by anticholinesterase pesticides, (2) induction of hepatic microsomal cytochromes P450 by chemicals such as PAHs and PCBs, (3) reproductive problems such as terata and eggshell thinning, and (4) aberrations of hemoglobin synthesis, including the effects of lead and of certain chlorinated hydrocarbons. Many studies on DNA damage and of histopathological effects, particularly in the form of tumors, have already been completed. There are presently numerous other opportunities for field validation. Bile metabolites of contaminants in fish reveal exposure to contaminants that might otherwise be difficult to detect or quantify. Bile analysis is beginning to be extended to species other than fishes. Assessment of oxidative damage and immune competence appear to be valuable biomarkers. needing only additional field validation for wider use. The use of metallothioneins as biomarkers depends on the development of convenient, inexpensive methodology that provides information not available from measurements of metal ions. The use of stress proteins as biomarkers depends on development of convenient, inexpensive methodology and field validation. Gene arrays and proteomics hold promise as bioindicators for contaminant exposure or effect, particularly because of the large amount of data that could be generated, but they still need extensive development and testing.

Book chapter

Natural offshore oil seepage and related tarball accumulation on the California coastline — Santa Barbara Channel and the southern Santa Maria Basin; source identification and inventory

Oil spillage from natural sources is very common in the waters of southern California. Active oil extraction and shipping is occurring concurrently within the region and it is of great interest to resource managers to be able to distinguish between natural seepage and anthropogenic oil spillage. The major goal of this study was to establish the geologic setting, sources, and ultimate dispersal of natural oil seeps in the offshore southern Santa Maria Basin and Santa Barbara Basins. Our surveys focused on likely areas of hydrocarbon seepage that are known to occur between Point Arguello and Ventura, California. Our approach was to 1) document the locations and geochemically fingerprint natural seep oils or tar; 2) geochemically fingerprint coastal tar residues and potential tar sources in this region, both onshore and offshore; 3) establish chemical correlations between offshore active seeps and coastal residues thus linking seep sources to oil residues; 4) measure the rate of natural seepage of individual seeps and attempt to assess regional natural oil and gas seepage rates; and 5) interpret the petroleum system history for the natural seeps. To document the location of sub-sea oil seeps, we first looked into previous studies within and near our survey area. We measured the concentration of methane gas in the water column in areas of reported seepage and found numerous gas plumes and measured high concentrations of methane in the water column. The result of this work showed that the seeps were widely distributed between Point Conception east to the vicinity of Coal Oil Point, and that they by in large occur within the 3-mile limit of California State waters. Subsequent cruises used sidescan and high resolution seismic to map the seafloor, from just south of Point Arguello, east to near Gaviota, California. The results of the methane survey guided the exploration of the area west of Point Conception east to Gaviota using a combination of seismic instruments. The seafloor was mapped by sidescan sonar, and numerous lines of high -resolution seismic surveys were conducted over areas of interest. Biomarker and stable carbon isotope ratios were used to infer the age, lithology, organic matter input, and depositional environment of the source rocks for 388 samples of produced crude oil, seep oil, and tarballs mainly from coastal California. These samples were used to construct a chemometric fingerprint (multivariate statistics) decision tree to classify 288 additional samples, including tarballs of unknown origin collected from Monterey and San Mateo County beaches after a storm in early 2007. A subset of 9 of 23 active offshore platform oils and one inactive platform oil representing a few oil reservoirs from the western Santa Barbara Channel were used in this analysis, and thus this model is not comprehensive and the findings are not conclusive. The platform oils included in this study are from west to east: Irene, Hildago, Harvest, Hermosa, Heritage, Harmony, Hondo, Holly, Platform A, and Hilda (now removed). The results identify three “tribes” of 13 C-rich oil samples inferred to originate from thermally mature equivalents of the clayey-siliceous, carbonaceous marl, and lower calcareous-siliceous members of the Monterey Formation. Tribe 1 contains four oil families having geochemical traits of clay-rich marine shale source rock deposited under suboxic conditions with substantial higher-plant input. Tribe 2 contains four oil families with intermediate traits, except for abundant 28,30-bisnorhopane, indicating suboxic to anoxic marine marl source rock with hemipelagic input. Tribe 3 contains five oil families with traits of distal marine carbonate source rock deposited under anoxic conditions with pelagic but little or no higher-plant input. Tribes 1 and 2 occur mainly south of Point Conception in paleogeographic settings where deep burial of the Monterey Formation source rock favored generation from all three members or their equivalents. In this area, oil from the clayey-siliceous and carbonaceous marl members (Tribes 1 and 2) may overwhelm that from the lower calcareous-siliceous member (Tribe 3) because the latter is thinner and less oil-prone than the overlying members. Tribe 3 occurs mainly north of Point Conception, where shallow burial caused preferential generation from the underlying lower calcareous-siliceous member or another unit with similar characteristics. It is very desirable to be able to clearly distinguish the naturally occurring seep oils from the anthropogenically derived platform oils. Within the “training set” of oils and tars (388 samples), the biomarker parameters are sometimes sufficient to allow unique discrimination of individual platform oils. More often however, platform samples and seep samples with sources geographically close to each other are too similar to each other, with respect to the biomarker parameters, to definitively differentiate them on that basis alone. In some cases other parameters can be helpful. These other parameters are related to the degree of biogeochemical degradation or weathering that the oils or tars have experienced. These components include the typical oil distribution of n-alkane hydrocarbons and isoprenoids pristane and phytane. All of the platform oils in our sample set contain these components. On the other hand, the seep oils or tars have been exposed to significant biodegradation while in the near subsurface. The majority, but not all of seep oils or tars have been biodegraded up to or beyond the loss of n-alkanes and isoprenoids. Seep oils found in the vicinity of Coal Oil Point or Arroyo Burro are apparently the least weathered and are particularly likely to retain significant n-alkanes and isoprenoids. Therefore the combination of chemometric fingerprinting and the presence or absence of n-alkanes and isoprenoids help to differentiate anthropogenic production oils versus natural seeps oils and tars. The differentiation is not always definitive because of the close chemical similarity of some samples and the variability in the biodegradation progression. This is the case near Coal Oil Point, and near Platform A (Dos Cuadros Field) where seep oils and Platform Holly and Platform A oils are genetically very similar and cannot be definitively distinguished after a period of a few days of weathering. In contrast, oils from the Point Conception platforms can be distinguished on the basis of chemometric fingerprinting alone. In the middle of this spectrum are oils from Platforms Harmony, Heritage, and Hondo, where it is expected that oil weathering would take on the order of two weeks to a month to produce tarballs similar to those seen near Point Conception. In this case there is a much greater degree of weathering needed to proceed from produced oil to the biodegraded tar characteristic of tarball stranded on the beach. Tar deposition on beaches was monitored as part of cooperative with the County of Santa Barbara Energy Division and the U.S. Geological Survey during 2001-2003. We found tar deposition varies on a seasonal basis. In general, tarballs accumulate at a faster rate or remain longer on all beaches during the summer and fall months. The reasons for this are unclear based on our limited observations, however we speculate that factors such as prevailing winds and currents combined with more quiescent wave conditions favors the accumulation and preservation of tarballs on the beach during the summer and fall months. In contrast, winter storms, with much greater wave action remove beach sand and other materials, and stormy seas tend to break up oil that might weather into tarballs. Natural seepage is affected by the spring/neap tidal cycle; however, the link to tar deposition is unclear. Longer periods of monitoring are needed to address the variability in the data and provide a more robust statistical analysis.

California

Differential expression profiles of microRNA in the little brown bat (Myotis lucifugus) associated with white nose syndrome affected and unaffected individuals

First documented in New York State in 2006, white nose syndrome (WNS) quickly became the leading cause of mortality in hibernating bat species in the United States. WNS is caused by a psychrophilic fungus, Geomyces destructans. Clinical signs of this pathogen are expressed as a dusty white fungus predominately around the nose and on the wings of affected bats. Relatively new biomarkers, such as microRNAs (miRNAs) are being targeted as markers to predict the syndrome prior to the clinical manifestation. The primary objective of this study was to identify miRNAs that could serve as biomarkers and proxies of little brown bat health. Bats were collected from hibernacula that had tested positive and negative for WNS. Genetic sequencing was completed using the Ion Torrent platform. A number of miRNAs were identified from the liver as putative biomarkers of WNS. However, given the small sample size for each treatment, this data set has only coarsely identified miRNAs indicative of WNS, and further validation is required.

Open-File Report

Bioindicators used in aquatic and terrestrial monitoring

There are many different types of contaminants present in the environment ranging from synthetic chemicals, which would not be present in the environment without man's intervention, to trace metals that are required for life. Concerns range from possible harmful effects on flora and fauna to possible harm to humans consuming such organisms. The complete chemical analysis for all possible environmental contaminants in sediments, water, air, and every species and sample of interest would not only be excessively costly, but the facilities to handle do many samples do not exist. Such chemical analysis would only establish the presence of contaminants, without revealing how available or active they were within the organism. Bioindicators, sometimes called biomarkers , are responses in living organisms that may simply signify exposure to contaminants, may predict future harm, or may themselves be harmful effects. In this chapter, a bioindicator will be interpreted to mean the same as a biomarker (a biochemical, physiological, or morphological response), but not a population or ecosystem bioindicator such as a sentinel species, genetic variability, or species richness. thus, a bioindicator (biomarker) may be studied in a particular species to assess the status of that species, or in a sentinel species to assess habitat status. Individuals of the sentinel species might be those already residing at the site of interest or might be pristine organisms brought to the site and maintained in cages (fish) or released and recovered (birds).

Book chapter

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU

The portion of the Snake River fall Chinook Salmon Oncorhynchus tshawytscha ESU that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2017 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, (3) USGS use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses, and (4) the detection of 8-mm PIT tags at Lower Granite Dam. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence has been relatively stable; whereas the timing of parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier as apparent abundance of juveniles has increased. Growth rate (g/d) and dispersal size of parr also declined as apparent abundance of juveniles increased. Passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster as estimated abundance of fall Chinook Salmon smolts in Lower Granite Reservoir has increased. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use the information covered here in a comprehensive modeling effort to conduct action effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management RM&E. In 2017, the USGS searched 15 shallow water spawning sites in conjunction with the Idaho Power Company (IPC). Redd counts agreed with those of IPC for a little more than half the sites suggesting that we need more training in redd counting. We recovered 67 carcasses, and tissue samples are currently being analyzed for parentage to ultimately determine the percentage of hatchery-origin spawners on the spawning grounds. Redd fading was examined to determine the frequency at which aerial surveys should be conducted. Most redds surveyed through time were visible for at least 4 weeks after the redd was initially constructed. Redd fading was variable amongst sites and depended on location. In 2017, we conducted a second year of evaluating detection efficiency of 8-mm PIT tags in the Lower Granite Dam juvenile fish collection system. Groups of 75–78 fish were tagged with 8-mm Biomark, 8-mm Oregon RFID, 9-mm Biomark, and 12-mm Biomark PIT tags and released into the bypass upstream of the upwell. From 97.4 to 100% (depending on tag type) of tagged fish were detected on at least one antenna in the Lower Granite Dam bypass system. Mean detection efficiency within the predominant passage route (i.e., diversion river exit) exceeded 0.98 for all tag types in both years. These results suggest that fish tagged in the field with 8-mm PIT tags should be detected at rates similar to larger tags at main-stem hydroelectric dams.

Snake River Basin

RNA sequencing analysis of transcriptional change in the freshwater mussel Elliptio complanata after environmentally relevant sodium chloride exposure

To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled sodium chloride (NaCl) exposures. Ribonucleic acid sequencing (RNA-Seq) of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for 7 d, of which 290 had nonoverlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism. The rate-limiting enzyme for synthesis of taurine, an amino acid frequently linked to osmotic stress in aquatic species, was upregulated, as was the transmembrane ion pump sodium/potassium adenosine 5′-triphosphatase. These patterns confirm a primary transcriptional response to the experimental dose, albeit likely overlapping with nonspecific secondary stress responses. Substantial involvement of the heat shock protein 70 chaperone family and the water-transporting aquaporin family was not detected, however, in contrast to some studies in other bivalves. A subset of the most significantly regulated genes was confirmed by quantitative polymerase chain reaction in an independent sample. Cluster analysis showed separation of mussels exposed to 2 ppt NaCl from control mussels in multivariate space, but mussels exposed to 1 ppt NaCl were largely indistinguishable from controls. Transcriptome-scale analysis of salt exposure under laboratory conditions efficiently identified candidate biomarkers for further functional analysis and field validation

Environmental Toxicology and Chemistry

Tools to minimize interlaboratory variability in vitellogenin gene expression monitoring programs

The egg yolk precursor protein vitellogenin is widely used as a biomarker of estrogen exposure in male fish. However, standardized methodology is lacking and little is known regarding the reproducibility of results among laboratories using different equipment, reagents, protocols, and data analysis programs. To address this data gap we tested the reproducibility across laboratories to evaluate vitellogenin gene ( vtg ) expression and assessed the value of using a freely available software data analysis program. Samples collected from studies of male fathead minnows ( Pimephales promelas ) exposed to 17α-ethinylestradiol (EE2) and minnows exposed to processed wastewater effluent were evaluated for vtg expression in 4 laboratories. Our results indicate reasonable consistency among laboratories if the free software for expression analysis LinRegPCR is used, with 3 of 4 laboratories detecting vtg in fish exposed to 5 ng/L EE2 ( n = 5). All 4 laboratories detected significantly increased vtg levels in 15 male fish exposed to wastewater effluent compared with 15 male fish held in a control stream. Finally, we were able to determine that the source of high interlaboratory variability from complementary deoxyribonucleic acid (cDNA) to quantitative polymerase chain reaction (qPCR) analyses was the expression analysis software unique to each real-time qPCR machine. We successfully eliminated the interlaboratory variability by reanalyzing raw fluorescence data with independent freeware, which yielded cycle thresholds and polymerase chain reaction (PCR) efficiencies that calculated results independently of proprietary software. Our results suggest that laboratories engaged in monitoring programs should validate their PCR protocols and analyze their gene expression data following the guidelines established in the present study for all gene expression biomarkers.

Environmental Toxicology and Chemistry

Stress does not inhibit induced vitellogenesis in juvenile rainbow trout

Vitellogenin (Vtg) is a widely used biomarker for xenoestrogen exposure in male fishes. In female fishes Vtg can be negatively affected by stress independent of declines in estrogen. However, few data are available on the effect of stress in male fish abnormally producing Vtg, such as when exposed to xenoestrogens. The objective for these studies was to determine the effects of stress on fish forced to produce Vtg. Three weeks prior to the experiment immature juvenile rainbow trout, Oncorhynchus mykiss, were acclimated to the experimental tanks and fed a maintenance ration. We induced Vtg synthesis by injecting 17??-estradiol (E2) 7 days prior to experimentation. Treatments in duplicate tanks were: (1) no stressor; (2) stressor; (3) E 2; (4) E2 and stressor. Plasma was collected at time = 0 for baseline measurements from eight fish per tank and Vtg was significantly elevated in treated fish compared to uninjected controls. Water was drained from the stressor tanks then refilled to a level that just covered the backs of the fish. Eight fish were sampled again at 4 and 9 h, and 1, 7, and 14 days of continuous stress. Stressor tanks were refilled with water to pre-stress levels and the fish were sampled after another 2 weeks. Cortisol was significantly elevated from the unstressed fish at 4 h; however, plasma Vtg in the E 2-stimulated fish was not affected by the stressor at any timepoint. These results indicate that fish capture procedures employed in the field or caging experiments likely do not lead to false negative results when plasma Vtg is used as a biomarker for xenoestrogen exposure. It also suggests that the energetic load induced by stress is insufficient to cause a reduction in Vtg, during a continuous E2 administration, at least within the timepoints examined in this study. ?? 2006 Springer Science+Business Media, Inc.

Environmental Biology of Fishes

Chromosomal damage and EROD induction in tree swallows (Tachycineta bicolor) along the Upper Mississippi River, Minnesota, USA

The health of tree swallows, Tachycineta bicolor, on the Upper Mississippi River (UMR) was assessed in 2010 and 2011 using biomarkers at six sites downriver of Minneapolis/St. Paul, MN metropolitan area, a tributary into the UMR, and a nearby lake. Chromosomal damage was evaluated in nestling blood by measuring the coefficient of variation of DNA content (DNA CV) using flow cytometry. Cytochrome P450 1A activity in nestling liver was measured using the ethoxyresorufin- O -dealkylase (EROD) assay, and oxidative stress was estimated in nestling livers via determination of thiobarbituric acid reacting substances (TBARS), reduced glutathione (GSH), oxidized glutathione (GSSG), the ratio GSSG/GSH, total sulfhydryl, and protein bound sulfhydryl (PBSH). A multilevel regression model (DNA CV) and simple regressions (EROD and oxidative stress) were used to evaluate biomarker responses for each location. Chromosomal damage was significantly elevated at two sites on the UMR (Pigs Eye and Pool 2) relative to the Green Mountain Lake reference site, while the induction of EROD activity was only observed at Pigs Eye. No measures of oxidative stress differed among sites. Multivariate analysis confirmed an increased DNA CV at Pigs Eye and Pool 2, and elevated EROD activity at Pigs Eye. These results suggest that the health of tree swallows has been altered at the DNA level at Pigs Eye and Pool 2 sites, and at the physiological level at Pigs Eye site only.

Minnesota

Taxonomic, temporal, and spatial variations in zooplankton fatty acid composition in Puget Sound, WA, USA

Fatty acid (FA) content and composition of zooplankton in Puget Sound, Washington (USA) was studied to investigate the nutritional quality of diverse zooplankton prey for juvenile salmon ( Oncorhynchus spp.) in terms of their essential fatty acid (EFA) content. The study focus was on eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and arachidonic acid (ARA) as these are key FA needed to maintain growth and development of juvenile fish. The different zooplankton taxa varied in their FA composition. Much of the variation in FA composition was driven by 18:1ω9 (a biomarker of carnivory), ARA, DHA, and FA characteristic of diatoms, which are linked to zooplankton diet sources. Gammarid and hyperiid amphipods contained the highest amount of EFA, particularly the gammarid amphipod Cyphocaris challengeri , while shrimp and copepods had much lower EFA content. Crab larvae, which are important prey for juvenile salmon in Puget Sound, had intermediate EPA + DHA content and the lowest DHA/EPA ratio, and were rich in diatom biomarkers. Temporal and spatial trends in zooplankton lipids were less apparent than the taxonomic differences, although the EFA content increased from spring to summer in Cancridae zoeae and the amphipod C. challengeri . These results on taxon-specific EFA content provide baseline information on the nutritional quality of zooplankton that can be applied in food web models. Combining zooplankton fatty acid data (quality) with taxon-specific zooplankton biomass data (quantity) enables development of new, sensitive indicators of juvenile fish production to help assess recent declines in salmon production in the Pacific Northwest and predict future adult returns.

Washington

Geochemical imprint of depositional conditions on organic matter in laminated—Bioturbated interbeds from fine-grained marine sequences

Laminated organic-rich shales are interbedded at a scale of centimeters to a few meters with bioturbated organic-poor mudstones or limestones in some fine-grained marine sequences. We have analyzed the organic matter in pairs of laminated/bioturbated interbeds from Cretaceous and Devonian rocks deposited in epicontinental and oceanic settings for the purpose of studying the influence of depositional and early diagenetic environment on the organic geochemical properties of marine shales. Results of these analyses indicate that for rocks that are still in a diagenetic stage of thermal alteration, the relative abundance of biomarker compounds and specific biomarker indices can be useful indicators of depositional and early diagenetic conditions. Pristane/phytane ratios are generally highest for laminated rocks from epicontinental basins and appear to reflect the input of isoprenoid precursors more than oxygenated versus anoxic depositional conditions. The thermally immature laminated rocks are characterized by relatively high contents of 17β(H), 21β(H)-hopanes, hopenes, sterenes and diasterenes, and by strong predominance of the 22R over 22S homohopane isomers. Thermally immature bioturbated samples are characterized by absence of the β,β-hopanes, by low contents of both saturated and unsaturated polycyclic hydrocarbons, and by slight or no predominance of the 22R over 22S homohopane isomers. There are less obvious compositional differences between the saturated hydrocarbons in the laminated and bioturbated units from the thermally mature sequences. For both the thermally mature and immature laminated samples, the degree of isomerization at the 22 C position for hopanes and at the 20 C position for steranes is generally consistent with the degree of thermal maturity interpreted from other properties of the organic matter. The bioturbated samples, however, exhibit inconsistent and anomalously high degrees of isomerization for the homohopanes, resulting either from reworking and oxidation of the primary organic matter or from the presence of older recycled organic matter.

Marine Geology