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At least 253 records · Page 14Linked to original sources
USGS2000

Defining anural malformations in the context of a developmental problem

This paper summarizes terminology and general concepts involved in animal development for the purpose of providing background for the study and understanding of frog malformations. The results of our radiographic investigation of rear limb malformations in Rana pipiens provide evidence that frog malformations are the product of early developmental errors. Although bacteria, parasites and viruses were identified in these metamorphosed frogs, the relevant window to look for the teratogenic effect of these agents is in the early tadpole stage during limb development. As a result, our microbiological findings must be regarded as inconclusive relative to determining their contribution to malformations because we conducted our examinations on metamorphosed frogs not tadpoles. Future studies need to look at teratogenic agents (chemical, microbial, physical or mechanical) that are present in the embryo, tadpole, and their environments at the stages of development that are relevant for the malformation type. The impact of these teratogenic agents then needs to be assessed in appropriate animal models using studies that are designed to mimic field conditions. The results of these laboratory tests should then be analyzed in such a way that will allow comparison with the findings in the wild-caught tadpoles and frogs.

Journal of the Iowa Academy of Science↗
USGS2010

Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

Little is known about the distribution and abundance of viruses in deep-sea cold-seep environments. Like hydrothermal vents, seeps support communities of macrofauna that are sustained by chemosynthetic bacteria. Sediments close to these communities are hypothesized to be more microbiologically active and therefore to host higher numbers of viruses than non-seep areas. Push cores were taken at five types of Gulf of Mexico habitats at water depths below 1000 m using a remotely operated vehicle (ROV). The habitats included non-seep reference sediment, brine seeps, a microbial mat, an urchin field, and a pogonophoran worm community. Samples were processed immediately for enumeration of viruses and prokaryotes without the addition of a preservative. Prokaryote counts were an order of magnitude lower in sediments directly in contact with macrofauna (urchins, pogonophorans) compared to all other samples (10 7 vs. 10 8 cells g -1 dry weight) and were highest in areas of elevated salinity (brine seeps). Viral-Like Particle (VLP) counts were lowest in the reference sediments and pogonophoran cores (10 8 VLP g -1 dry wt), higher in brine seeps (10 9 VLP g -1 dry wt), and highest in the microbial mats (10 10 VLP g -1 dry wt). Virus-prokaryote ratios (VPR) ranged from <5 in the reference sediment to >30 in the microbial mats and >60 in the urchin field. VLP counts and VPR were all significantly greater than those reported from sediments in the deep Mediterranean Sea and in most cases were higher than recent data from a cold-seep site near Japan. The high VPR suggest that greater microbial activity in or near cold-seep environments results in greater viral production and therefore higher numbers of viruses.

Gulf Of Mexico;Green Canyon;Atwater Valley;Alamino↗
USGS2007

Southern California Bight 2003 Regional Monitoring Program: V. water quality

More than $30 million is expended annually on environmental monitoring in the Southern California Bight (SCB), yet only 5% of the Bight is monitored on an ongoing basis. Therefore, environmental managers in the SCB decided to expand their monitoring program and, starting in 1994, decided to conduct periodic regional assessments of ecosystem condition and assess the overall health of the SCB. Sixty-five different organizations collaborated in 2003 to create the third SCB Regional Monitoring Program (Bight '03). Bight '03 was designed to be integrated regional monitoring program that encompasses regulatory, academic, and non-governmental agencies. Bight '03 had three components: Coastal Ecology, Shoreline Microbiology, and Water Quality. This report addresses the purpose, approach, findings, and recommendations from the Water Quality component, which focused on contamination-laden stormwater runoff, in particularly its variability in time and space as well as its short-term ecological impacts. Specifically, the Bight '03 Water Quality component had three primary goals, the first of which was to described the temporal evolution of stormwater plumes produced by the major southern California rivers. Specifically, the study was intended to determine how far offshore the plumes extended, how rapidly they advected, how long before the plumes dispersed and how these properties differed among storms and river systems. The second goal was to describe how the physical properties (e.g., turbidity, temperature, salinity) of the plume related to biogeochemical and ecological properties that are of more direct concern to the water quality management community. Accomplished primarily through ship-based sampling of water quality parameters, this second goal was to describe how far offshore, and for how ;long after the storm, elevated bacterial concentrations, toxicity, and nutrients could be detected. Similar to the fist goal, the study also addressed how these answers differed among storms and river systems. The final goal was to determine whether relationships between environmental indicators derived from coincident satellite remote sensing and in situ data sets are sufficiently robust for remote sensing to become a routine water quality monitoring programs. Remote sensing data potentially provide coastal managers with synoptic near-real time regional information about prevailing ocean conditions and hazards that would complement existing field-based sampling protocols, but only if there is a thorough understanding of how to interpret and utilize the proxy measures, such as ocean color. The understanding of these priorities through Bight '03 sampling is intended to provide the basis for developing more efficient, widespread and coast-effective coastal ocean monitoring techniques. Water quality data were collected across eight major river systems within four geographic regions of southern California. Field measurements included the primary contaminants of interest, i.e., bacterial concentrations, water toxicity, and nutrients, as well as related parameters such as temperatures, salinity, total suspended solids, transmissivity, chlorophyll, and colored dissolved organic material (CDOM) concentrations. For each of the four major regions, i.e., Santa Clara/Ventura Rivers, Ballona Creek/Santa Monica Bay, San Pedro Shelf, and the San Diego, Tijuana Rivers, two stormwater events were sampled for up to three days by ship resulting in 574 water column CTD+ profiles and 705 discrete water samples during 36 ship-days. These data were analyzed in combination with MODIS ocean color satellite remote sensing, buoy meteorological observations, drifters, and HF radar current measurements to evaluate the dispersal patterns, dynamics, and impacts of the freshwater runoff plumes. Based on these data and resulting analyses, the principal conclusions were as follow: - Stormwater runoff turbidity plumes were found to be spatially extensive, covering up to 2500 km 2 within the Southern California Bight nearshore zone, and persisting over the entire duration of the post-storm sampling period (at least 3 days). - The spatial and temporal extent of the portion of the plume with contaminants was far less than that of the turbidity plume, typically representing <10% of its area (30-70% off Tijuana); however, with contaminant impacts generally greatly reduced or absent by the third or fourth day of sampling - Pseudo-nitzschia , a harmful algae that produces domoic acid, was found to be more abundant than previously reported. - Accurately describing stormwater runoff plumes requires a combination of in situ and remote sensing assessment tools, with satellite data providing valuable synoptic information. From these conclusions, the following recommendations are provided: - Future studies designed to describe stormwater plumes should include a combination of ship - and remote sensing-based methods. - CDOM is a good proxy of the freshwater runoff plume and should be added as a standard measurement parameter on water quality instrument packages. - Investigations are needed that assess on a local basis the spatial extent of ecological effects of stormwater plumes early in the storm, ideally accompanied by airborne imagery to provide improved temporal & spatial resolution, to fill in knowledge gaps. The next Bight regional monitoring program should focus on quantifying nutrient loadings and dynamics in association with stormwater runoff and other sources, and characterize their attendant ecosystem impacts such as phytoplankton blooms.

California↗
USGS2015

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

Limestone cedar glades are a type of rock outcrop ecosystem characterized by shallow soil and extreme hydrologic conditions—seasonally ranging from xeric to saturated—that support a number of plant species of conservation concern. Although a rich botanical literature exists on cedar glades, soil biochemical processes and the ecology of soil microbial communities in limestone cedar glades have largely been ignored. This investigation documents the abiotic stress regime of this ecosystem (shallow soil, extreme hydrologic fluctuations and seasonally high soil surface temperatures) as well as soil physical and chemical characteristics, and relates both types of information to ecological structures and functions including vegetation, soil respiration, and soil microbial community metabolic profiles and diversity. Methods used in this investigation include field observations and measurements of soil physical and chemical properties and processes, laboratory analyses, and microbiological assays of soil samples. Stress factors quantified by this research include shallow soil (depth to bedrock ranging from 2.4 to 22.6 cm), volumetric soil water content levels seasonally ranging from xeric (below 5%) to saturated (above 50%), and seasonally extreme ground-surface temperatures (above 48°C). Findings from this research indicate that spatial and temporal heterogeneity exists in limestone cedar glades in terms of abiotic stress factors and soil physical and chemical properties. Several such soil properties (e.g. soil depth, organic matter levels, pH, and particle size distribution) are spatially correlated. These soil properties were statistically related to ecological structures and functions such as vegetation patterns, soil respiration, the density of culturable heterotrophic microbes in soil and metabolic diversity of soil microbial community profiles. In general, zones within limestone cedar glades that had relatively shallow soil, alkaline pH, low levels of organic matter and high levels of silt also tended to have depressed rates of soil respiration and reduced densities and metabolic diversity of culturable heterotrophic soil microbes. Additionally, seasonally-relevant stress factors including soil water content and temperatures at or near the soil surface were related to the same set of ecological structures and functions.

Tennessee↗
USGS2017

Final data report for factors controlling DDE dechlorination rates on the Palos Verdes Shelf: A field and laboratory investigation

This data report provides a compilation of information developed over the last 6+ years by a multi-disciplinary, multi-institutional research team. The overall goal of this work has been to identify the biological, chemical, and physical factors that control rates of reductive dechlorination of DDE and DDMU in sediments of the Palos Verdes Shelf (PVS). More specific questions and objectives are delineated in the Scope of Work (section 12.1., Appendix 1). The study was composed of two parts: 1) field characterization studies, and 2) laboratory microcosm experiments. The goal of the field characterization studies was to define the conditions under which reductive dechlorination of DDE (and DDMU) is occurring in PVS sediments. This involved two separate cruises (2009, 2010) during which sediment cores, bottom water and other real-time field measurements (e.g., conductivity, temperature, depth of the water column) were acquired. The sediment cores were distributed among research team members for detailed chemical (R. Eganhouse, B. Orem, M. Reinhard), microbiological (A. Spormann), and physical (B. Edwards) analysis as well as for laboratory microcosm experiments (M. Reinhard). A team of collaborating USGS scientists generously contributed valuable information pertaining to geochronology (P. Swarzenski), the character of sedimentary geosorbent phases (P. Hackley), mineralogy (D. Webster), and grain-size characteristics (C. Sherwood) of PVS sediment samples. Together, this information will serve as framework for a conceptual model of natural degradation processes in the DDT-contaminated sediments on the PVS. These findings will enable the USEPA to gain a better understanding of the controls on reductive dechlorination and how dechlorination rates vary spatially and temporally. This, in turn, should facilitate decision making concerning the progress of natural attenuation and when monitoring at the site can be terminated. Toward that end, a brief Synthesis Report, summarizing and interpreting the acquired data, is being prepared and will be released in the coming year.

Palos Verdes Shelf↗
USGS2017

Challenges in recovering resources from acid mine drainage

Metal recovery from mine waters and effluents is not a new approach but one that has occurred largely opportunistically over the last four millennia. Due to the need for low-cost resources and increasingly stringent environmental conditions, mine waters are being considered in a fresh light with a designed, deliberate approach to resource recovery often as part of a larger water treatment evaluation. Mine water chemistry is highly dependent on many factors including geology, ore deposit composition and mineralogy, mining methods, climate, site hydrology, and others. Mine waters are typically Ca-Mg-SO4±Al±Fe with a broad range in pH and metal content. The main issue in recovering components of these waters having potential economic value, such as base metals or rare earth elements, is the separation of these from more reactive metals such as Fe and Al. Broad categories of methods for separating and extracting substances from acidic mine drainage are chemical and biological. Chemical methods include solution, physicochemical, and electrochemical technologies. Advances in membrane techniques such as reverse osmosis have been substantial and the technique is both physical and chemical. Biological methods may be further divided into microbiological and macrobiological, but only the former is considered here as a recovery method, as the latter is typically used as a passive form of water treatment.

Conference Paper↗
USGS2002

USGS leads United States effort in Mallik Well

This winter, in the extremely cold, far reaches of the upper Northwest Territory of Canada, there is an international consortium of researchers participating in a program to study methane hydrates. The researchers are currently drilling a 1200 m-deep production research well through the permafrost. It is one of three wells located in the Mackenzie Delta, on the shore of the Beaufort Sea. Two observation wells were drilled adjacent to the main production test well earlier this year. Research objectives for the program focus on two themes: (1) the assessment of the production and properties of gas hydrates, and (2) an assessment of the stability of continental gas hydrates given warming trends predicted by climate change models. Of particular interest is the physical response of the gas hydrate to depressurization and thermal production stimulation. Cores are being taken from the well, and scientists hope to retrieve at least 200 m of core, including all the gas hydrate-rich intervals. Once cored, the samples are transported 200 kilometers over ice roads to Inuvik. Nearly 60 researchers are examining the cores for everything from geophysical parameters to microbiological analyses.

Fire in the Ice: NETL Methane Hydrate Newsletter↗
USGS1998

Anaerobic oxidation of [1,2-14C]dichloroethene under Mn(IV)-reducing conditions

Anaerobic oxidation of [1,2- 14 C]dichloroethene to 14 CO 2 under Mn(IV)-reducing conditions was demonstrated. The results indicate that oxidative degradation of partially chlorinated solvents like dichloroethene can be significant even under anoxic conditions and demonstrate the potential importance of Mn(IV) reduction for remediation of chlorinated groundwater contaminants.

Applied and Environmental Microbiology↗
USGS1966

Uptake of 2,4-dichlorophenoxyacetic acid by Pseudomonas fluorescens

Factors influencing the uptake of the sodium salt of 2,4-dichlorophenoxyacetic acid (2,4-D), under conditions in which no net metabolism occurred, were investigated in an effort to determine both the significance of “non-metabolic” uptake as a potential agent in reducing pesticide levels and the mechanisms involved. Uptake of 2,4-D was affected by p H, temperature, and the presence of other organic and inorganic compounds. Uptake was more pronounced at p H values less than 6, which implies that there may be some interaction between charged groups on the cell and the ionized carboxyl group of 2,4-D. Active transport, carrier-mediated diffusion, passive diffusion, and adsorption were considered as possible mechanisms. Though uptake was inhibited by glucose, sodium azide, and fluorodinitrobenzene (but not by uranyl ion), 2,4-D was not accumulated against a concentration gradient, a necessary consequence of an active transport system, nor was isotope counterflow found to occur. Thus, carrier-mediated diffusion was finally precluded, implying that uptake probably occurs by a two-step process: sorption onto the cell wall followed by passive diffusion into the cytoplasm.

Applied Microbiology↗
USGS1993

Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn (IV), U (VI), and nitrate. In whole cell suspensions, the c -type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans . The name Geobacter metallireducens is proposed.

Archives of Microbiology↗
USGS1985

Isolation of anaerobic oxalate-degrading bacteria from freshwater lake sediments

Enrichment cultures that anaerobically degraded oxalate were obtained from lake sediment inocula. From these, 5 pure cultures of anaerobic oxalate-degrading bacteria were isolated and partially characterized. The isolates were Gram-negative, non-sporeforming, non-motile, obligate anaerobes. Oxalate was required for growth and was stoichiometrically converted to formate; 14 CO 2 was also recovered when 14 C-oxalate was added. Maximal growth occurred when the oxalate concentration was 50 mM. Acetate stimulated growth in the presence of oxalate, however, 14 C-experiments indicated that acetate was only utilized for cell carbon. The isolates were either spiral-shaped or rod-shaped organisms. The first morphotype grew much more slowly than the second and exhibited 13-fold lower cell yields. These isolates represent a new strain of oxalate-degrading bacteria. The second morphotype was similar to the anaerobic oxalate-degrading bacteria previously found in rumen. This report extends the known habitats in which anaerobic oxalate-degrading organisms have been found to include aquatic sediments.

Archives of Microbiology↗
USGS1994

Anaerobic biodegradation of methyl esters by Acetobacterium woodii and Eubacterium limosum

The ability of Acetobacterium woodii and Eubacterium limosum to degrade methyl esters of acetate, propionate, butyrate, and isobutyrate was examined under growing and resting-cell conditions. Both bacteria hydrolyzed the esters to the corresponding carboxylates and methanol under either condition. Methanol was further oxidized to formate under growing but not resting conditions. Unlike the metabolism of phenylmethylethers, no H 2 requirement was evident for ester biotransformation. The hydrolysis of methyl carboxylates is thermodynamically favorable under standard conditions and the mixotrophic metabolism of ester/CO 2 allowed for bacterial growth. These results suggest that the degradation of methyl carboxylates may be a heretofore unrecognized nutritional option for acetogenic bacteria.

Journal of Industrial Microbiology↗
USGS1995

Remediation of uranium contaminated soils with bicarbonate extraction and microbial U(VI) reduction

A process for concentrating uranium from contaminated soils in which the uranium is first extracted with bicarbonate and then the extracted uranium is precipitated with U(VI)-reducing microorganisms was evaluated for a variety of uranuum-contaminated soils. Bicarbonate (100 mM) extracted 20–94% of the uranium that was extracted with nitric acid. The U(VI)-reducing microorganism, Desulfovibrio desulfuricans reduced the U(VI) to U(IV) in the bicarbonate extracts. In some instances unidentified dissolved extracted components, presumably organics, gave the extract a yellow color and inhibited U(VI) reduction and/or the precipitation of U(IV). Removal of the dissolved yellow material with the addition of hydrogen peroxide alleviated this inhibition. These results demonstrate that bicarbonate extraction of uranium from soil followed by microbial U(VI) reduction might be an effective mechanism for concentrating uranium from some contaminated soils.

Journal of Industrial Microbiology↗
USGS1996

Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAl-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c -type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAl-1 differs from all other described bacteria, and represents the type strain of a new genus and species, Geovibrio ferrireducens .

Archives of Microbiology↗
USGS2001

Selenihalanaerobacter shriftii gen. nov., sp. nov., a halophilic anaerobe from Dead Sea sediments that respires selenate

We isolated an obligately anaerobic halophilic bacterium from the Dead Sea that grew by respiration of selenate. The isolate, designated strain DSSe-1, was a gram-negative, non-motile rod. It oxidized glycerol or glucose to acetate+CO2 with concomitant reduction of selenate to selenite plus elemental selenium. Other electron acceptors that supported anaerobic growth on glycerol were nitrate and trimethylamine-N-oxide; nitrite, arsenate, fumarate, dimethylsulfoxide, thiosulfate, elemental sulfur, sulfite or sulfate could not serve as electron acceptors. Growth on glycerol in the presence of nitrate occurred over a salinity range from 100 to 240 g/l, with an optimum at 210 g/l. Analysis of the 16S rRNA gene sequence suggests that strain DSSe-1 belongs to the order Halanaerobiales, an order of halophilic anaerobes with a fermentative or homoacetogenic metabolism, in which anaerobic respiratory metabolism has never been documented. The highest 16S rRNA sequence similarity (90%) was found with Acetohalobium arabaticum (X89077). On the basis of physiological properties as well as the relatively low homology of 16S rRNA from strain DSSe-1 with known genera, classification in a new genus within the order Halanaerobiales, family Halobacteroidaceae is warranted. We propose the name Selenihalanaerobacter shriftii. Type strain is strain DSSe-1 (ATCC accession number BAA-73).

Archives of Microbiology↗
USGS2024

Microbial communities in standing dead trees in ghost forests are largely aerobic, saprophytic, and methanotrophic

Standing dead trees (snags) are recognized for their influence on methane (CH 4 ) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH 4 fluxes were highly variable (− 0.11–0.51 mg CH 4 m −2 h −1 ). CH 4 production was measured in three out of ten snags; whereas, CH 4 consumption was measured in two out of ten snags. Potential CH 4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH 4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH 4 g −1 h −1 , respectively. Four cores oxidized CH 4 under oxic conditions, with an average rate of − 1.13 ± 0.31 ng CH 4 g −1 h −1 . Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH 4 -cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH 4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH 4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.

Current Microbiology↗
USGS2002

Microbial transformation of elements: The case of arsenic and selenium

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.

International Microbiology↗