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At least 793 records · Page 44Linked to original sources

USGS1989

Salinity variations in submarine hydrothermal systems by layered double-diffusive convection

Various mechanisms have been proposed to explain the salinity variations in vent fluids of seafloor geothermal systems. New experiments reacting diabase and evolved seawater were carried out to reproduce earlier published observations of Cl depletions attributed to formation of an ephemeral Cl-bearing mineral. The absence of any Cl depletions in the present study suggests that the formation of Cl-bearing minerals is not sufficiently widespread to account for the observed salinity variations in the vent fluids. A re-evaluation of both field and laboratory evidence has led to a new model for subseafloor circulation that accounts for salinity variations as well as other chemical and mineralogic observations. In place of a simple single-pass convection system, we propose that the seafloor systems consist of two vertically nested convection cells in which a brine layer at depth heats and drives an overlying seawater cell. Such layering of salinities, a process known in fluid mechanics as double-diffusive convection, is an expected result when convection is induced in saline fluids. The process provides for stable high-temperature heat transfer upward from the cracking front adjacent to the magma, and for limited chemical exchange of the brine with the overlying seawater to explain salinity variations and high metal contents in the vent fluids. The brine also provides an effective medium to produce the secondary mineral assemblages observed in rocks from the mid-ocean ridges and ophiolites unsuccessfully produced in laboratory studies using seawater. The brine originates from the two-phase separation of seawater during magmatic/tectonic events and accumulates and remains relatively stable in the region immediately above the magma chamber.

Journal of Geology↗

USGS2026

Deep subsurface organic-rich shale supports abundant, diverse, and novel fungi

As Earth’s principal reservoir of organic carbon and microbial biomass, the deep subsurface hosts microorganisms capable of mobilizing this once-sequestered carbon. Contrary to standard assumptions of eukaryotic scarcity, this study documents abundant fungal communities, ranging from 4.2 × 10 3 to 6.8 × 10 3 fungal cells mL −1 , across a methane-producing organic-rich shale 247–556 meters below the surface. Although fungal:bacterial cell ratios ranged from 1:7028 to 1:713, application of biomass conversion factors developed for oceanic systems yielded a median fungal:bacterial biomass ratio of 1:4.7. 16S rRNA gene amplicons revealed bacterial and archaeal communities mirroring those found in well-characterized extremophilic, carbon-degrading environments, while sequencing of 18S rRNA gene and ITS rRNA spacer amplicons collectively identified a eukaryotic hotspot with 689 fungal OTUs across six phyla. The dominant fungal classes, Agaricomycetes and Dothideomycetes, are well-established degraders of recalcitrant carbon compounds at the surface, suggesting they may similarly contribute to organic matter degradation and ecosystem maintenance in the subsurface. Cultivation and isolation efforts yielded 205 fungal strains, including 13 candidate novel taxa, underscoring the deep subsurface as an underexplored eukaryotic habitat. Stable carbon isotopes indicate methane is predominantly generated via microbial conversion of the fossil carbon, while water isotopes suggest in situ geochemical conditions have been relatively stable since the Late Pleistocene, with subglacial recharge as a plausible mechanism for microbial introduction. Collectively, these findings suggest that fungi are underrecognized contributors to organic matter transformation and functional diversity in the deep biosphere, revealing a critical gap in our understanding of deep subsurface ecosystem processes.

Indiana, Michigan, Ohio↗

USGS2016

Complementary approaches to diagnosing marine diseases: a union of the modern and the classic

Linking marine epizootics to a specific aetiology is notoriously difficult. Recent diagnostic successes show that marine disease diagnosis requires both modern, cutting-edge technology (e.g. metagenomics, quantitative real-time PCR) and more classic methods (e.g. transect surveys, histopathology and cell culture). Here, we discuss how this combination of traditional and modern approaches is necessary for rapid and accurate identification of marine diseases, and emphasize how sole reliance on any one technology or technique may lead disease investigations astray. We present diagnostic approaches at different scales, from the macro (environment, community, population and organismal scales) to the micro (tissue, organ, cell and genomic scales). We use disease case studies from a broad range of taxa to illustrate diagnostic successes from combining traditional and modern diagnostic methods. Finally, we recognize the need for increased capacity of centralized databases, networks, data repositories and contingency plans for diagnosis and management of marine disease.

Philosophical Transactions of the Royal Society B:↗

USGS2007

Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor

A facultative chemoautotrophic bacterium, strain MLHE-1 T , was isolated from Mono Lake, an alkaline hypersaline soda lake in California, USA. Cells of strain MLHE-1 T were Gram-negative, short motile rods that grew with inorganic electron donors (arsenite, hydrogen, sulfide or thiosulfate) coupled with the reduction of nitrate to nitrite. No aerobic growth was attained with arsenite or sulfide, but hydrogen sustained both aerobic and anaerobic growth. No growth occurred when nitrite or nitrous oxide was substituted for nitrate. Heterotrophic growth was observed under aerobic and anaerobic (nitrate) conditions. Cells of strain MLHE-1 T could oxidize but not grow on CO, while CH 4 neither supported growth nor was it oxidized. When grown chemoautotrophically, strain MLHE-1 T assimilated inorganic carbon via the Calvin–Benson–Bassham reductive pentose phosphate pathway, with the activity of ribulose 1,5-bisphosphate carboxylase (RuBisCO) functioning optimally at 0.1 M NaCl and at pH 7.3. Strain MLHE-1 T grew over broad ranges of pH (7.3–10.0; optimum, 9.3), salinity (15–190 g l −1 ; optimum 30 g l −1 ) and temperature (13–40 °C; optimum, 30 °C). Phylogenetic analysis of 16S rRNA gene sequences placed strain MLHE-1 T in the class Gammaproteobacteria (family Ectothiorhodospiraceae ) and most closely related to Alkalispirillum mobile (98.5 %) and Alkalilimnicola halodurans (98.6 %), although none of these three haloalkaliphilic micro-organisms were capable of photoautotrophic growth and only strain MLHE-1 T was able to oxidize As(III). On the basis of physiological characteristics and DNA–DNA hybridization data, it is suggested that strain MLHE-1 T represents a novel species within the genus Alkalilimnicola for which the name Alkalilimnicola ehrlichii is proposed. The type strain is MLHE-1 T (=DSM 17681 T =ATCC BAA-1101 T ). Aspects of the annotated full genome of Alkalilimnicola ehrlichii are discussed in the light of its physiology.

California↗

USGS2015

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska

In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (< 0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.

Alaska↗

USGS2019

Fire disturbance influences endangered Cape Sable Seaside Sparrow (Ammopiza maritima mirabilis) relative bird count

Periodicity of fire disturbance is a known driver of ecosystem function and is reported as important in both promoting and maintaining viable breeding habitat for the endangered Cape Sable Seaside Sparrow ( Ammospiza maritima mirabilis ; CSSS). In south Florida, the CSSS serves as a fine-scale indicator of the marl and mixed-marl prairie communities of the Florida Everglades. The CSSS distribution is affected by numerous well-documented physical drivers, including water depth and fire regime. Here, we fit zero-inflated negative binomial generalized linear mixed models and used model selection to determine the relationship between CSSS bird count observations from 1992 to 2014 and the spatially-specific fire return interval on the landscape. CSSS bird count was highest at a 5–8-year fire return interval and increased linearly with the percent of cell burned (400 × 400 m cells). The results of this study can inform management plans designed to maintain existing, and promote new, marl prairie habitat for conservation of the CSSS.

Florida↗

USGS2019

A simple method for simulating groundwater interactions with fens to forecast development effects

Protection of fens–wetlands dependent on groundwater discharge–requires characterization of groundwater sources and stresses. Because instrumentation and numerical modeling of fens is labor intensive, easy-to-apply methods that model fen distribution and their vulnerability to development are desirable. Here we demonstrate that fen areas can be simulated using existing steady-state MODFLOW models when the unsaturated zone flow (UZF) package is included. In cells where the water table is near land surface, the UZF package calculates a head difference and scaled conductance at these “seepage drain” cells to generate average rates of vertical seepage to the land. This formulation, which represents an alternative to blanketing the MODFLOW domain with drains, requires very little input from the user because unsaturated flow-routing is inactive and results are primarily driven by easily obtained topographic information. Like the drain approach, it has the advantage that the distribution of seepage areas is not predetermined by the modeler, but rather emerges from simulated heads. Beyond the drain approach, it takes account of intracell land surface variation to explicitly quantify multiple surficial flows corresponding to infiltration, rejected recharge, recharge and land-surface seepage. Application of the method to a basin in southeastern Wisconsin demonstrates how it can be used as a decision-support tool to first, reproduce fen distribution and, second, forecast drawdown and reduced seepage at fens in response to shallow pumping.

Wisconsin↗

USGS2025

A new groundwater energy transport model for the MODFLOW hydrologic simulator

Heat transport in the subsurface is an important aspect of research related to the effects of a warming climate on ecological services (i.e., cold-water refugia); the development of geothermal resources for energy banking schemes (i.e., aquifer thermal energy storage [ATES]); and the effects of temperature on other aspects of groundwater quality, such as nutrient cycling. Historically, simulation of heat transport using the MODFLOW groundwater simulator and related codes was performed by scaling the input parameters of a solute-transport model to emulate heat transport. However, that approach required additional pre- and post-processing of input and output and could not account for the variation in effective thermal storage and transport properties during transient, unsaturated flow, for example. True heat-transport capabilities in the context of MODFLOW were first introduced in a variant called USG-Transport. More recently, a new groundwater energy-transport (GWE) model type has been added to MODFLOW 6, the core version of the MODFLOW hydrologic simulator. GWE supports the simulation of heat transport on structured or unstructured grids as well as within and between features of advanced packages that represent streams, lakes, multi-aquifer wells, and the unsaturated zone. GWE is integrated within MODFLOW 6 and is accessible through the FloPy Python package and the MODFLOW 6 application programming interface (API). An example simulation demonstrates conduction between grid cells through both the water and the solid aquifer material, including thermal bleeding from saturated overburden cells into a groundwater flow field.

Groundwater↗

USGS2006

In kittiwakes food availability partially explains the seasonal decline in humoral immunocompetence

The immune system plays an important role in fitness, and interindividual variation in immunocompetence is due to several factors including food supply. Seasonal variation in food resources may therefore explain why immunocompetence in bird nestlings usually declines throughout the breeding season, with chicks born early in the season receiving more food than chicks born later, and thereby possibly developing a more potent immune system. Although there are studies supporting this hypothesis, none has been experimental. We performed an experiment in the kittiwake Rissa tridactyla by manipulating the food supply of pairs that were left to produce a first brood, and of pairs that were induced to produce a late replacement brood. If food supply mediates, at least partially, seasonal variations in chick immunocompetence, non‐food‐supplemented chicks would show a stronger seasonal decline in immunocompetence than food‐supplemented chicks. Food supplementation improved humoral immunocompetence (the production of immunoglobulins Y), but not T‐cell immunocompetence (phytohaemagglutinin, PHA response). T‐cell immunocompetence of food‐supplemented and non‐food‐supplemented chicks decreased through the season but to a similar extent, whereas the humoral immunocompetence of non‐food‐supplemented chicks decreased more strongly than that of food‐supplemented chicks. Our results suggest that the seasonal decline in humoral immunocompetence can be explained, at least partly, by variations in food supply throughout the breeding season.

Alaska↗

USGS2010

Climatic water deficit, tree species ranges, and climate change in Yosemite National Park

Aim (1) To calculate annual potential evapotranspiration (PET), actual evapotranspiration (AET) and climatic water deficit (Deficit) with high spatial resolution; (2) to describe distributions for 17 tree species over a 2300-m elevation gradient in a 3000-km 2 landscape relative to AET and Deficit; (3) to examine changes in AET and Deficit between past ( c. 1700), present (1971–2000) and future (2020–49) climatological means derived from proxies, observations and projections; and (4) to infer how the magnitude of changing Deficit may contribute to changes in forest structure and composition. Location Yosemite National Park, California, USA. Methods We calculated the water balance within Yosemite National Park using a modified Thornthwaite-type method and correlated AET and Deficit with tree species distribution. We used input data sets with different spatial resolutions parameterized for variation in latitude, precipitation, temperature, soil water-holding capacity, slope and aspect. We used climate proxies and climate projections to model AET and Deficit for past and future climate. We compared the modelled future water balance in Yosemite with current species water-balance ranges in North America. Results We calculated species climatic envelopes over broad ranges of environmental gradients – a range of 310 mm for soil water-holding capacity, 48.3°C for mean monthly temperature (January minima to July maxima), and 918 mm yr −1 for annual precipitation. Tree species means were differentiated by AET and Deficit, and at higher levels of Deficit, species means were increasingly differentiated. Modelled Deficit for all species increased by a mean of 5% between past ( c. 1700) and present (1971–2000). Projected increases in Deficit between present and future (2020–49) were 23% across all plots. Main conclusions Modelled changes in Deficit between past, present and future climate scenarios suggest that recent past changes in forest structure and composition may accelerate in the future, with species responding individualistically to further declines in water availability. Declining water availability may disproportionately affect Pinus monticola and Tsuga mertensiana . Fine-scale heterogeneity in soil water-holding capacity, aspect and slope implies that plant water balance may vary considerably within the grid cells of kilometre-scale climate models. Sub-grid-cell soil and topographical data can partially compensate for the lack of spatial heterogeneity in gridded climate data, potentially improving vegetation-change projections in mountainous landscapes with heterogeneous topography.

Journal of Biogeography↗

USGS2006

Cellular immune response in rainbow trout Salmo gairdneri Richardson to Yersinia ruckeri O-antigen monitored by the passive haemolytic plaque assay test

The specificity and kinetics of the immune response of rainbow trout ( Salmo gairdneri ) to single injections of an O-antigen extracted from the bacterial pathogen Yersinia ruckeri , which causes enteric redmouth in fish, were investigated by the passive haemolytic plaque assay and serum antibody quantitation. Doses ranging from 5 ng to 500 mg in 10-fold increments were injected intraperitoneally into groups of trout held at 17 × 1°5°C. The occurrence of plaque forming cells (PFC) and humoral antibody was followed for 35 days after injection. Trout gave an immune response to doses of 500 ng and above. Seven days after injection no humoral antibody was detected, but PFC were found in the spleen. The maximum PFC numbers occurred 11 days after injection. On day 21, few PFC were found, whereas serum antibody titres were highest. The antibody from immunized trout showed little or no cross-reactions with sheep red blood cells passively labelled With antigens from other fish pathogens.

Journal of Fish Diseases↗

USGS2010

Uncovering a latent multinomial: Analysis of mark–recapture data with misidentification

Natural tags based on DNA fingerprints or natural features of animals are now becoming very widely used in wildlife population biology. However, classic capture-recapture models do not allow for misidentification of animals which is a potentially very serious problem with natural tags. Statistical analysis of misidentification processes is extremely difficult using traditional likelihood methods but is easily handled using Bayesian methods. We present a general framework for Bayesian analysis of categorical data arising from a latent multinomial distribution. Although our work is motivated by a specific model for misidentification in closed population capture-recapture analyses, with crucial assumptions which may not always be appropriate, the methods we develop extend naturally to a variety of other models with similar structure. Suppose that observed frequencies f are a known linear transformation f=A'x of a latent multinomial variable x with cell probability vector pi= pi(theta). Given that full conditional distributions [theta | x] can be sampled, implementation of Gibbs sampling requires only that we can sample from the full conditional distribution [x | f, theta], which is made possible by knowledge of the null space of A'. We illustrate the approach using two data sets with individual misidentification, one simulated, the other summarizing recapture data for salamanders based on natural marks.

Biometrics↗

USGS2007

The occurrence of hepatozoon in the gray squirrel (Sciurus carolinensis)

Hepatozoon sciuri (Coles, 1914) is reported from gray squirrels ( Sciurus carolinensis ) in Washington, D.C. and Maryland. Blood smears stained with Giemsa's stain revealed a parasitemia in 16 to 71% of the squirrels examined. A technique for laking the red cells and concentrating the white cells in blood samples demonstrated this protozoon to be present in every squirrel so tested.

Maryland↗

USGS1989

Development, characterization, and use of monoclonal and polyclonal antibodies against the myxosporean, Ceratomyxa shasta

Both monoclonal and polyclonal antisera were produced against Ceratomyxa shasta. Ascites containing trophozoites of the parasite was collected from infected fish and used as antigen for immunization of mice. The resulting monoclonal antibodies reacted specifically with trophozoite and sporoblast stages but did not react with C. shasta spores by either indirect fluorescent antibody techniques or in Western blots. This indicates that some C. shasta antigens are specific to certain life stages of the parasite. Polyclonal antiserum was produced in a rabbit by injecting a spore protein electro-eluted from an SDS-polyacrylamide gel. This antiserum reacted with both trophozoites and spores by indirect fluorescent antibody techniques and in Western blots. All antisera were tested for cross-reactivity to trout white blood cells, a contaminant of the ascites, and to other myxosporea. Two monoclonal antibodies reacted with white blood cells and myxosporea of the genera Sphaerospora and Myxobilatus. One hybridoma produced antibodies of high specificity for C. shasta pre-spore stages. This is the first report of a monoclonal antibody produced against a myxosporean parasite.

Journal of Eukaryotic Microbiology↗

USGS2005

Simulating reservoir leakage in ground-water models

Leakage to ground water resulting from the expansion and contraction of reservoirs cannot be easily simulated by most ground-water flow models. An algorithm, entitled the Reservoir Package, was developed for the United States Geological Survey (USGS) three-dimensional finite-difference modular ground-water flow model MODFLOW. The Reservoir Package automates the process of specifying head-dependent boundary cells, eliminating the need to divide a simulation into many stress periods while improving accuracy in simulating changes in ground-water levels resulting from transient reservoir stage. Leakage between the reservoir and the underlying aquifer is simulated for each model cell corrresponding to the inundated area by multiplying the head difference between the reservoir and the aquifer with the hydraulic conductance of the reservoir-bed sediments.

Groundwater↗

USGS2005

Bacterial transport experiments in fractured crystalline bedrock

The efficiency of contaminant biodegradation in ground water depends, in part, on the transport properties of the degrading bacteria. Few data exist concerning the transport of bacteria in saturated bedrock, particularly at the field scale. Bacteria and microsphere tracer experiments were conducted in a fractured crystalline bedrock under forced-gradient conditions over a distance of 36 m. Bacteria isolated from the local ground water were chosen on the basis of physicochemical and physiological differences (shape, cell-wall type, motility), and were differentially stained so that their transport behavior could be compared. No two bacterial strains transported in an identical manner, and microspheres produced distinctly different breakthrough curves than bacteria. Although there was insufficient control in this field experiment to completely separate the effects of bacteria shape, reaction to Gram staining, cell size, and motility on transport efficiency, it was observed that (1) the nonmotile, mutant strain exhibited better fractional recovery than the motile parent strain; (2) Gram-negative rod-shaped bacteria exhibited higher fractional recovery relative to the Gram-positive rod-shaped strain of similar size; and (3) coccoidal (spherical-shaped) bacteria transported better than all but one strain of the rod-shaped bacteria. The field experiment must be interpreted in the context of the specific bacterial strains and ground water environment in which they were conducted, but experimental results suggest that minor differences in the physical properties of bacteria can lead to major differences in transport behavior at the field scale.

Ground Water↗

USGS2010

A hybrid finite-difference and analytic element groundwater model

Regional finite-difference models tend to have large cell sizes, often on the order of 1–2 km on a side. Although the regional flow patterns in deeper formations may be adequately represented by such a model, the intricate surface water and groundwater interactions in the shallower layers are not. Several stream reaches and nearby wells may occur in a single cell, precluding any meaningful modeling of the surface water and groundwater interactions between the individual features. We propose to replace the upper MODFLOW layer or layers, in which the surface water and groundwater interactions occur, by an analytic element model (GFLOW) that does not employ a model grid; instead, it represents wells and surface waters directly by the use of point-sinks and line-sinks. For many practical cases it suffices to provide GFLOW with the vertical leakage rates calculated in the original coarse MODFLOW model in order to obtain a good representation of surface water and groundwater interactions. However, when the combined transmissivities in the deeper (MODFLOW) layers dominate, the accuracy of the GFLOW solution diminishes. For those cases, an iterative coupling procedure, whereby the leakages between the GFLOW and MODFLOW model are updated, appreciably improves the overall solution, albeit at considerable computational cost. The coupled GFLOW–MODFLOW model is applicable to relatively large areas, in many cases to the entire model domain, thus forming an attractive alternative to local grid refinement or inset models.

Groundwater↗

USGS2009

Hematology of the West Indian manatee (Trichechus manatus)

Hemograms on blood obtained from 10 clinically normal West Indian Manatees ( Trichechus manatus ) were studied. The red cells were large and in lower number than in most terrestrial species. The manatee does not have a neutrophil as is present in most species, but it has a heterophil whose granules stain pink with the Wright-Giemsa stain. The eosinophil has uniform red-staining granules that make its differentiation from heterophils difficult. Both large and small lymphocytes, monocytes and basophils are present. The total number of white blood cells was comparable to that of common domestic species as were the platelet numbers. No reticulocytes were found.

Veterinary Clinical Pathology↗