Heterogeneous occupancy and density estimates of the pathogenic fungus Batrachochytrium dendrobatidis in waters of North America.

Biodiversity losses are occurring worldwide due to a combination of stressors. For example, by one estimate, 40% of amphibian species are vulnerable to extinction, and disease is one threat to amphibian populations. The emerging infectious disease chytridiomycosis, caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd), is a contributor to amphibian declines worldwide.

Integration of stable carbon isotope, microbial community, dissolved hydrogen gas, and ²HH₂O tracer data to assess bioaugmentation for chlorinated ethene degradation in fractured rocks.

An in situ bioaugmentation (BA) experiment was conducted to understand processes controlling microbial dechlorination of trichloroethene (TCE) in groundwater at the Naval Air Warfare Center (NAWC), West Trenton, NJ. In the BA experiment, an electron donor (emulsified vegetable oil and sodium lactate) and a chloro-respiring microbial consortium were injected into a well in fractured mudstone of Triassic age. Water enriched in ²H was also injected as a tracer of the BA solution, to monitor advective transport processes.

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation.

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic.

Arsenic speciation in food chains from mid-Atlantic hydrothermal vents.

Arsenic concentration and speciation were determined in benthic fauna collected from the Mid-Atlantic Ridge hydrothermal vents. The shrimp species, , the vent chimney-dwelling mussel, , , a commensal worm of , and the gastropod showed variations in As concentration and in stable isotope (δC and δN) signature between species, suggesting different sources of As uptake. Arsenic speciation showed arsenobetaine to be the dominant species in , whereas in arsenosugars were most abundant, although arsenobetaine, dimethylarsinate, and inorganic arsenic were also observed, along with several unidentified species.

Evidence for iron-mediated anaerobic methane oxidation in a crude oil-contaminated aquifer.

In a methanogenic crude oil contaminated aquifer near Bemidji, Minnesota, the decrease in dissolved CH(4) concentrations along the groundwater flow path, along with the positive shift in δ(13) C(CH) (4) and negative shift in δ(13) C(DIC) , is indicative of microbially mediated CH(4) oxidation. Calculations of electron acceptor transport across the water table, through diffusion, recharge, and the entrapment and release of gas bubbles, suggest that these processes can account for at most 15% of the observed total reduced carbon oxidation, including CH(4) . In the anaerobic plume, the characteristic Fe(III)-reducing genus Geobacter was the most abundant of the microbial groups tested, and depletion of labile sediment iron is observed over time, confirming that reduced carbon oxidation coupled to iron reduction is an important process.

Impact disruption and recovery of the deep subsurface biosphere.

Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the ∼35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control.

Methane oxidation in a crude oil contaminated aquifer: Delineation of aerobic reactions at the plume fringes.

High resolution direct-push profiling over short vertical distances was used to investigate CH(4) attenuation in a petroleum contaminated aquifer near Bemidji, Minnesota. The contaminant plume was delineated using dissolved gases, redox sensitive components, major ions, carbon isotope ratios in CH(4) and CO(2), and the presence of methanotrophic bacteria. Sharp redox gradients were observed near the water table.

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge.

To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR).

Distribution limits of Batrachochytrium dendrobatidis: a case study in the Rocky Mountains, USA.

Knowledge of the environmental constraints on a pathogen is critical to predicting its dynamics and effects on populations. Batrachochytrium dendrobatidis (Bd), an aquatic fungus that has been linked with widespread amphibian declines, is ubiquitous in the Rocky Mountains. As part of assessing the distribution limits of Bd in our study area, we sampled the water column and sediments for Bd zoospores in 30 high-elevation water bodies that lacked amphibians.

Quantitative PCR detection of Batrachochytrium dendrobatidis DNA from sediments and water.

The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease implicated in amphibian declines on 5 continents. Polymerase chain reaction (PCR) primer sets exist with which amphibians can be tested for this disease, and advances in sampling techniques allow non-invasive testing of animals. We developed filtering and PCR based quantitative methods by modifying existing PCR assays to detect Bd DNA in water and sediments, without the need for testing amphibians; we tested the methods at 4 field sites.

Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray.

The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition.

A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents.

Deep-sea hydrothermal vents are important in global biogeochemical cycles, providing biological oases at the sea floor that are supported by the thermal and chemical flux from the Earth's interior. As hot, acidic and reduced hydrothermal fluids mix with cold, alkaline and oxygenated sea water, minerals precipitate to form porous sulphide-sulphate deposits. These structures provide microhabitats for a diversity of prokaryotes that exploit the geochemical and physical gradients in this dynamic ecosystem.

Detection of Helicobacter pylori and fecal indicator bacteria in five North American rivers.

This study examines the use of fecal indicator bacteria (FIB) as a predictor of the presence of Helicobacter spp. A combination of standard culture and molecular techniques were used to detect and quantify FIB, Helicobacter spp. and H.

Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent.

The phylogenetic diversity was determined for a microbial community obtained from an in situ growth chamber placed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge (23 degrees 22' N, 44 degrees 57' W). The chamber was deployed for 5 days, and the temperature within the chamber gradually decreased from 70 to 20 degrees C. Upon retrieval of the chamber, the DNA was extracted and the small-subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific for the Archaea or Bacteria domain and cloned.

Geomicrobiology of subglacial ice above Lake Vostok, Antarctica.

Data from ice 3590 meters below Vostok Station indicate that the ice was accreted from liquid water associated with Lake Vostok. Microbes were observed at concentrations ranging from 2.8 x 10(3) to 3.

Amplification, cloning, and sequencing of a nifH segment from aquatic microorganisms and natural communities.

By use of the polymerase chain reaction and degenerate oligonucleotide primers for highly conserved regions of nifH, a segment of nifH DNA was amplified from several aquatic microorganisms, including an N2-fixing bacterium closely associated with the marine filamentous cyanobacterium Trichodesmium sp., a heterotrophic isolate from the root/rhizome of the seagrass Ruppia maritima, and the heterocystous freshwater cyanobacterium Anabaena oscillarioides. nifH segments were amplified directly from DNA extracted from the rhizosphere of roots of the seagrass Halodule wrightii.

The Malmö polymorphism of coagulation factor IX, an immunologic polymorphism due to dimorphism of residue 148 that is in linkage disequilibrium with two other F.IX polymorphisms.

A mouse monoclonal antibody (MAB 9.9) to coagulation factor IX (F.IX) detects a polymorphism in the plasma of normal people.

Population genetics of coagulant factor IX: frequencies of two DNA polymorphisms in five ethnic groups.

Two frequently used restriction-enzyme polymorphisms (RFLPs) of coagulant F.IX, TaqI and XmnI, have been examined in five ethnic groups: white Americans, black Americans, East Indians, Chinese, and Malays. There is a distinct "cline" in the frequencies of both polymorphisms, from white Americans to Malays.

Leishmania donovani: immunization against infection as a function of parasite growth phase.

C57BL/6 mice were immunized against Leishmania donovani infection with a subcutaneous vaccination protocol. Groups received 3 injections at 4-day intervals combining glucan and killed promastigotes harvested from either logarithmic or stationary phase cultures. Controls were immunized with glucan alone, stationary or log phase promastigotes alone, or were untreated.