Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Cells”

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 1,567 records · Page 87Linked to original sources

Streamlined approach for assessing embedded consumption of lithium and cobalt in the United States

In today's complex global supply chains, time and data intensive analyses are required to understand global flows of mineral commodities from mine to consumer, particularly for mineral commodities in products (electronics, automobiles, etc.) that contain multiple parts with many mineral commodities. National and regional analyses require additional time and data to incorporate international trade flows. However, data limitations and time constraints often prohibit global and national material flow analyses for minor metals. Here we present a methodological approach to circumvent these constraints by utilizing readily available industry-level global data from the United Nations Statistics Division and national industrial data to estimate total requirements for a mineral commodity. We apply this approach to lithium and cobalt use in the United States for the year 2018 and distinguish between apparent raw material consumption versus inferred embedded consumption of lithium and cobalt materials in all forms. The results show that more than half of the United States’ total requirements for both lithium and cobalt is in parts and products that were manufactured outside the United States. In large part, this is due to limited US manufacturing capability for lithium-ion battery materials and cells and the United States’ high import reliance for electronics that use those batteries.

Journal of Industrial Ecology↗

Temperature mediates secondary dormancy in resting cysts of Pyrodinium bahamense (Dinophyceae)

High‐biomass blooms of the toxic dinoflagellate Pyrodinium bahamense occur most summers in Tampa Bay, Florida, USA, posing a recurring threat to ecosystem health. Like many dinoflagellates, P. bahamense forms immobile resting cysts that can be deposited on the seafloor—creating a seed bank that can retain the organism within the ecosystem and initiate future blooms when cysts germinate. In this study, we examined changes in the dormancy status of cysts collected from Tampa Bay and applied lessons from plant ecology to explore dormancy controls. Pyrodinium bahamense cysts incubated immediately after field collection displayed a seasonal pattern in dormancy and germination that matched the pattern of cell abundance in the water column. Newly deposited (surface) cysts and older (buried) cysts exhibited similar germination patterns, suggesting that a common mechanism regulates dormancy expression in new and mature cysts. Extended cool‐ and warm‐temperature conditioning of field‐collected cysts altered the cycle of dormancy compared with that of cysts in nature, with the duration of cool temperature exposure being the best predictor of when cysts emerged from dormancy. Extended warm conditioning, on the other hand, elicited a return to dormancy, or secondary dormancy, in nondormant cysts. These results directly demonstrate environmental induction of secondary dormancy in dinoflagellates—a mechanism common and thoroughly documented in higher plants with seasonal growth cycles. Our findings support the hypothesis that a seasonal cycle in cyst germination drives P. bahamense bloom periodicity in Tampa Bay and point to environmentally induced secondary dormancy as an important regulatory factor of that cycle.

Florida↗

Bet-hedging and best-bet strategies shape seed dormancy

Seed dormancy (i.e. delayed germination even when conditions are favourable) is a key plant characteristic that occurs among many species worldwide. But, what selective pressures led to seed dormancy? A recent study provides a major analysis of the factors driving this trait at the global scale (Zhang et al ., 2022 ). Using c. 12 000 species and 10 million records across the globe, they conclude that dormancy is a strategy for plants living under ‘seasonal/unpredictable’ environments; and suggest that bet-hedging could be the major mechanism behind the pattern. To reach their conclusions the authors relate the proportion of species with dormant seeds in a grid-cell global map against climate variables related to annual precipitation, temperature and seasonality. Then they showed that the most significant variables were those related to climate seasonality that they equate with unpredictable climates (although seasonal climates usually are highly predictable in their seasonal cycles).

New Phytologist↗

Diversity of anaerobic halophilic microorganisms

Life in the presence of high salt concentrations is compatible with life in the absence of oxygen. Halophilic and halotolerant anaerobic prokaryotes are found both in the archaeal and in the bacterial domain, and they display a great metabolic diversity. Many of the representatives of the Halobacteriales (Archaea), which are generally considered aerobes, have the potential of anaerobic growth. Some can use alternative electron acceptors such as nitrate, fumarate, dimethylsulfoxide or trimethylamine-N-oxide Halobacterium salinarum can also grow fermentatively on L-arginine, and bacteriorhodopsin-containing cells may even grow anaerobically, energized by light. Obligatory anaerobic halophilic methanogenic Archaea also exist. The bacterial domain contains many anaerobic halophiles, including sulfate reducers. There is also a group of specialized obligatory anaerobic Bacteria, phylogenetically clustering in the low G+C branch of the Firmicutes. Most representatives of this group (order Haloanaerobiales , families Haloanaerobiaceae and Halobacteroidaceae ) are fermentative, using a variety of carbohydrates and amino acids. One species combines the potential for anaerobic growth at high salt concentrations with a preference for high temperatures. Others are homoacetogens; Acetohalobium arabaticum can grow anaerobically as a chemolithotroph, producing acetate from hydrogen and CO 2 . The Haloanaerobiales accumulate high concentrations of K + and Cl - in their cytoplasm, thereby showing a strategy of salt adaptation similar to that used by the Halobacteriales . Recently a new representative of the Haloanaerobiales was isolated from bottom sediments of the Dead Sea (strain DSSe1), which grows anaerobically by oxidation of glycerol to acetate and CO 2 while reducing selenate to selenite and elementary selenium. Other electron acceptors supporting anaerobic growth of this strain are nitrate and trimethylamine- N -oxide. The versatility of life at high salt concentrations with respect to the variety of substrates used, the types of dissimilatory metabolism, and the diversity of potential electron acceptors has important implications for the potential for life in hostile environments lacking oxygen and high in salt, implications that may also be relevant to astrobiology.

Proceedings of SPIE↗

Localization and physical properties experiments conducted by Spirit at Gusev crater

The precise location and relative elevation of Spirit during its traverses from the Columbia Memorial station to Bonneville crater were determined with bundle-adjusted retrievals from rover wheel turns, suspension and tilt angles, and overlapping images. Physical properties experiments show a decrease of 0.2% per Mars solar day in solar cell output resulting from deposition of airborne dust, cohesive soil-like deposits in plains and hollows, bright and dark rock coatings, and relatively weak volcanic rocks of basaltic composition. Volcanic, impact, aeolian, and water-related processes produced the encountered landforms and materials.

Science↗

Localization and physical property experiments conducted by opportunity at Meridiani Planum

The location of the Opportunity landing site was determined to better than 10-m absolute accuracy from analyses of radio tracking data. We determined Rover locations during traverses with an error as small as several centimeters using engineering telemetry and overlapping images. Topographic profiles generated from rover data show that the plains are very smooth from meter- to centimeter-length scales, consistent with analyses of orbital observations. Solar cell output decreased because of the deposition of airborne dust on the panels. The lack of dust-covered surfaces on Meridiani Planum indicates that high velocity winds must remove this material on a continuing basis. The low mechanical strength of the evaporitic rocks as determined from grinding experiments, and the abundance of coarse-grained surface particles argue for differential erosion of Meridiani Planum.

Science↗

Thermal structure and dynamics of Saturn's northern springtime disturbance

Saturn’s slow seasonal evolution was disrupted in 2010–2011 by the eruption of a bright storm in its northern spring hemisphere. Thermal infrared spectroscopy showed that within a month, the resulting planetary-scale disturbance had generated intense perturbations of atmospheric temperatures, winds, and composition between 20° and 50°N over an entire hemisphere (140,000 kilometers). The tropospheric storm cell produced effects that penetrated hundreds of kilometers into Saturn’s stratosphere (to the 1-millibar region). Stratospheric subsidence at the edges of the disturbance produced “beacons” of infrared emission and longitudinal temperature contrasts of 16 kelvin. The disturbance substantially altered atmospheric circulation, transporting material vertically over great distances, modifying stratospheric zonal jets, exciting wave activity and turbulence, and generating a new cold anticyclonic oval in the center of the disturbance at 41°N.

Science↗

Time-lapse motion picture technique applied to the study of geological processes

Light-weight, battery-operated timers were built and coupled to 16-mm motion-picture cameras having apertures controlled by photoelectric cells. The cameras were placed adjacent to Emmons Glacier on Mount Rainier. The film obtained confirms the view that exterior time-lapse photography can be applied to the study of slow-acting geologic processes.

Washington↗

Dechlorination of DDT by Aerobacter aerogenes

Dechlorination of DDT to DDD in higher animals requires the presence of molecular oxygen, but in microorganisms the presence of oxygen hinders dechlorination. In cell-free preparations of Aerobacter aerogenes, the use of selected metabolic inhibitors indicated that reduced Fe(II) cytochrome oxidase was responsible for DDT dechlorination. This finding may possibly explain. the persistence of DDT residues in soils and sediments.

Science↗

Galileo infrared imaging spectroscopy measurements at Venus

During the 1990 Galileo Venus flyby, the Near Infrared Mapping Spectrometer investigated the night-side atmosphere of Venus in the spectral range 0.7 to 5.2 micrometers. Multispectral images at high spatial resolution indicate substantial cloud opacity variations in the lower cloud levels, centered at 50 kilometers altitude. Zonal and meridional winds were derived for this level and are consistent with motion of the upper branch of a Hadley cell. Northern and southern hemisphere clouds appear to be markedly different. Spectral profiles were used to derive lower atmosphere abundances of water vapor and other species.

Science↗

Geomicrobiology of subglacial ice above Lake Vostok, Antarctica

Data from ice 3590 meters below Vostok Station indicate that the ice was accredit from liquid water associated with Lake Vostok. Microbes were observed at concentrations ranging from 2.8 x 103 to 3.6 x 104 cells per milliliter; no biological incorporation of selected organic substrates or bicarbonate was detected. Bacterial 165 ribosomal DNA genes revealed low diversity in the gene population. The phylotypes were closely related to extant members of the alpha- and beta-Proteobacteria and the Actinomycetes. Extrapolation of the data from accretion ice to Lake Vostok implies that Lake Vostok may support a microbial population, despite more than 106 years of isolation from the atmosphere.

Science↗

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

INTRODUCTION Changes in the size and proportion of limbs and other structures have played a key role in the evolution of species. One common class of limb modification is recurrent wing reduction and loss of flight in birds. Indeed, Darwin used the occurrence of flightless birds as an argument in favor of his theory of natural selection. Loss of flight has evolved repeatedly and is found among 26 families of birds in 17 different orders. Despite the frequency of these modifications, we have a limited understanding of their underpinnings at the genetic and molecular levels. RATIONALE To better understand the evolution of changes in limb size, we studied a classic case of recent loss of flight in the Galapagos cormorant ( Phalacrocorax harrisi ). Cormorants are large water birds that live in coastal areas or near lakes, and P. harrisi is the only flightless cormorant among approximately 40 extant species. The entire population is distributed along the coastlines of Isabela and Fernandina islands in the Galapagos archipelago. P. harrisi has a pair of short wings, which are smaller than those of any other cormorant. The extreme reduction of the wings and pectoral skeleton observed in P. harrisi is an attractive model for studying the evolution of loss of flight because it occurred very recently; phylogenetic evidence suggests that P. harrisi diverged from its flighted relatives within the past 2 million years. We developed a comparative and predictive genomics approach that uses the genome sequences of P. harrisi and its flighted relatives to find candidate genetic variants that likely contributed to the evolution of loss of flight. RESULTS We sequenced and de novo assembled the whole genomes of P. harrisi and three closely related flighted cormorant species. We identified thousands of coding variants exclusive to P. harrisi and classified them according to their probability of altering protein function based on conservation. Variants most likely to alter protein function were significantly enriched in genes mutated in human skeletal ciliopathies, including Ofd1 , Evc , Wdr34 , and Ift122 . We carried out experiments in Caenorhabditis elegans to confirm that a missense variant present in the Galapagos cormorant IFT122 protein is sufficient to affect ciliary function. The primary cilium is essential for Hedgehog (Hh) signaling in vertebrates, and individuals affected by ciliopathies have small limbs and ribcages, mirroring the phenotype of P. harrisi . We also identified a 4–amino acid deletion in the regulatory domain of Cux1 , a highly conserved transcription factor that has been experimentally shown to regulate limb growth in chicken. The four missing amino acids are perfectly conserved in all birds and mammals sequenced to date. We tested the consequences of this deletion in a chondrogenic cell line and showed that it impairs the ability of CUX1 to transcriptionally up-regulate cilia-related genes (some of which contain function-altering variants in P. harrisi ) and to promote chondrogenic differentiation. Finally, we show that positive selection may have played a role in the fixation of the variants associated with loss of flight in P. harrisi . CONCLUSION Our results indicate that the combined effect of variants in genes necessary for the correct transcriptional regulation and function of the primary cilium likely contributed to the evolution of highly reduced wings and other skeletal adaptations associated with loss of flight in P. harrisi . Our approach may be generally useful for identification of variants underlying evolutionary novelty from genomes of closely related species.

Science↗

Winter phytoplankton dynamics in a subalpine lake, Colorado, U.S.A

The temporal dynamics of phytoplankton were examined in The Loch, a subalpine lake in Rocky Mountain National Park, over the winter seasons of 1987-88 and 1988-89. The Loch was ice-covered from early November until early to mid May. The pattern of phytoplankton biovolume during ice-cover was consistent between the two years with maxima occurring in November/December and February/March. This pattern resulted principally from the contribution of Asterionella formosa Hass. Other dominant phytoplankton species in terms of biomass ( Dinobryon sertularia Ehrenb., Cryptomonas ovata Ehrenb., and Peridinium cinctum (Müll.) Ehrenb.) collectively contributed from 10 to 90 % of the total cells. Algal composition changed throughout the winter and individual species varied in abundance with depth. The same dominant (and most of the rare) taxa were present both years. They varied in time of occurrence and abundance, but did not occur at the same time in both years. Phytoplankton species composition continually fluctuated throughout the winter. Because of the stability afforded by ice-cover, algal species succession was not driven by thermal regime or by wind induced changes in the mixed depth. Nor did grazing by the winter zooplankton assemblage, composed nearly exclusively of cyclopoid copepods and rotifers, adequately explain the phytoplankton dynamics. Freeze concentration of water (concentration as ions are excluded in the formation of ice) in early winter may be responsible for the early phytoplankton bloom.

Colorado↗

Nanoparticles formed from bacterial oxyanion reduction of toxic Group 15 and 16 metalloids

This chapter presents some examples of nanoparticles formed by only a few microbial species that are cultivated in only a handful of laboratories worldwide. The investigations so far have just scratched the surface of the potential of the natural world to yield bionanomineral producers. While future research should involve screening surveys of the prokaryotes for this biomineralizing phenomenon, more detailed investigations are justified. The chapter discusses microbial Interaction with Group 15 and 16 Toxic Metalloids. The toxicity of the metalloids Se, Te, and As is due to the disruption of thiol intracellular biochemistry through the formation of stable, long-lived sulfur complexes. Selenium oxyanion reduction occurs in a wide range of microbes, including representatives of the Wolinella , Pseudomonas , Sulfurospirillum , Enterobacter , Thaurea , Bacillus , Shewanella , and Citrobacter genera. Technological applications of Se(0) and Te(0) nanoparticles include their use in photocopiers, microelectronic circuits, and solar cells as a result of their photo-optical and semiconducting physical properties. Nonetheless, once novel Se, Te, and As bionanoparticles are identified as having significant technical applications, applied research into their practical commercial production will without doubt ensue rapidly.

Book chapter↗

Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan

Cladophora glomerata , a macrophytic green alga, is commonly found in the Great Lakes, and significant accumulations occur along shorelines during the summer months. Recently, Cladophora has been shown to harbor high densities of the fecal indicator bacteria Escherichia coli and enterococci. Cladophora may also harbor human pathogens; however, until now, no studies to address this question have been performed. In the present study, we determined whether attached Cladophora , obtained from the Lake Michigan and Burns Ditch (Little Calumet River, Indiana) sides of a breakwater during the summers of 2004 and 2005, harbored the bacterial pathogens Shiga toxin-producing Escherichia coli (STEC), Salmonella , Shigella , and Campylobacter . The presence of potential pathogens and numbers of organisms were determined by using cultural methods and by using conventional PCR, most-probable-number PCR (MPN-PCR), and quantitative PCR (QPCR) performed with genus- and toxin-specific primers and probes. While Shigella and STEC were detected in 100% and 25%, respectively, of the algal samples obtained near Burns Ditch in 2004, the same pathogens were not detected in samples collected in 2005. MPN-PCR and QPCR allowed enumeration of Salmonella in 40 to 80% of the ditch- and lakeside samples, respectively, and the densities were up to 1.6 &times; 10 3 cells per g Cladophora . Similarly, these PCR methods allowed enumeration of up to 5.4 &times; 10 2 Campylobacter cells/g Cladophora in 60 to 100% of lake- and ditchside samples. The Campylobacter densities were significantly higher (P < 0.05) in the lakeside Cladophora samples than in the ditchside Cladophora samples. DNA fingerprint analyses indicated that genotypically identical Salmonella isolates were associated with geographically and temporally distinct Cladophora samples. However, Campylobacter isolates were genetically diverse. Since animal hosts are thought to be the primary habitat for Campylobacter and Salmonella species, our results suggest that Cladophora is a likely secondary habitat for pathogenic bacteria in Lake Michigan and that the association of these bacteria with Cladophora warrants additional studies to assess the potential health impact on beach users.

Applied and Environmental Microbiology↗

Coupled arsenotrophy in a hot spring photosynthetic biofilm at Mono Lake, California

Red-pigmented biofilms grow on rock and cobble surfaces present in anoxic hot springs located on Paoha Island in Mono Lake. The bacterial community was dominated (∼ 85% of 16S rRNA gene clones) by sequences from the photosynthetic Ectothiorhodospira genus. Scraped biofilm materials incubated under anoxic conditions rapidly oxidized As(III) to As(V) in the light via anoxygenic photosynthesis but could also readily reduce As(V) to As(III) in the dark at comparable rates. Back-labeling experiments with 73 As(V) demonstrated that reduction to 73 As(III) also occurred in the light, thereby illustrating the cooccurrence of these two anaerobic processes as an example of closely coupled arsenotrophy. Oxic biofilms also oxidized As(III) to As(V). Biofilms incubated with [ 14 C]acetate oxidized the radiolabel to 14 CO 2 in the light but not the dark, indicating a capacity for photoheterotrophy but not chemoheterotrophy. Anoxic, dark-incubated samples demonstrated As(V) reduction linked to additions of hydrogen or sulfide but not acetate. Chemoautotrophy linked to As(V) as measured by dark fixation of [ 14 C]bicarbonate into cell material was stimulated by either H 2 or HS − . Functional genes for the arsenate respiratory reductase ( arrA ) and arsenic resistance ( arsB ) were detected in sequenced amplicons of extracted DNA, with about half of the arrA sequences closely related (∼98% translated amino acid identity) to those from the family Ectothiorhodospiraceae . Surprisingly, no authentic PCR products for arsenite oxidase ( aoxB ) were obtained, despite observing aerobic arsenite oxidation activity. Collectively, these results demonstrate close linkages of these arsenic redox processes occurring within these biofilms. Oxyanions of the group 15 element arsenic, arsenate [As(V)] and arsenite [As(III)], have been known for millennia to be potent poisons. Despite its well-established toxicity to life, the phenomenon of arsenic resistance was discovered whereby some microorganisms maintain an otherwise “normal” existence in the presence of high concentrations of As(V) or As(III) (17, 29, 31). More recently it has become recognized that certain representatives from the bacterial and archaeal domains can actually exploit the electrochemical potential of the As(V)/As(III) redox couple (+130 mV) to gain energy for growth. This can be achieved either by employing As(III) as an autotrophic electron donor or by using As(V) as a respiratory electron acceptor (18, 21, 34). The latter phenomenon, although most commonly associated with chemoheterotrophy, can also employ inorganic substances like sulfide or H 2 . Indeed, As(V)-respiring anaerobes displaying a capacity for chemoautotrophy with these electron donors have been isolated and described (5, 7, 16). We recently reported that photoautotrophy is supported by As(III) in anoxic biofilms located in hot springs on Paoha Island in Mono Lake, CA (15). This process represented a novel means of As(III) oxidation achieved via anoxygenic photosynthesis occurring in certain photosynthetic bacteria (i.e., Ectothiorhodospira ) and possibly within some cyanobacteria as well (e.g., “ Oscillatoria ”). Whether or not a microbial habitat is overtly oxic or anoxic, or temporally shifts between these two states over a diel cycle, critical energy linkages between aerobes and anaerobes have long been known for the biogeochemical cycles of key elements, such as sulfur, iron, and nitrogen. Most prominently studied is the case of nitrogen, whereby an ecological coupling exists between the processes of nitrification and denitrification (9, 10, 28). The former process provides energy to aerobic nitrifiers, while the latter process consumes the nitrate produced by this reaction, thereby meeting the energy needs of the denitrifiers. For arsenic, the detection of both As(III) oxidation and As(V) reduction in oxic and anoxic incubations of freshly collected periphyton suggested that an analogous coupled process may also occur for this element (12). Similarly, several uncontaminated soils in Japan displayed a capacity for either As(V) reduction or As(III) oxidation upon arsenic oxyanion amendment and whether they were incubated under oxic or anoxic conditions (39). A defined coculture consisting of an aerobic As(III) oxidizer (strain OL1) and an anaerobic As(V) respirer (strain Y5) was shown to function in this fashion under manipulated laboratory conditions of oxygen tension (26). We pursued the phenomenon of coupled arsenic metabolism further by using materials collected from the hot spring biofilms in Mono Lake, but we focused on examination of the cycling of arsenic under anoxic conditions. In this paper we report results obtained by manipulated incubations of red-pigmented biofilms found in the hot springs of Paoha Island. Preliminary community characterizations of these biofilms show that they are dominated by B acteria from the genus Ectothiorhodospira but also harbor an assemblage of Archaea related to the Halobacteriacaea . Incubation results have demonstrated the presence of the following arsenic metabolic activities: respiratory As(V) reduction, photosynthetic anaerobic As(III) oxidation, and aerobic As(III) oxidation, along with the ecophysiological conditions under which they occur. Surprisingly, we were unable to obtain authentic PCR products for arsenite oxidase genes ( aoxB ), despite observing aerobic As(III) oxidation activity. These biofilms serve as a model system for how anaerobic cycling of arsenic can be sustained with oxidation of As(III) by anoxygenic photosynthesis coupled to regeneration of this electron donor via dissimilatory As(V) reduction. The significance that such a light-driven anaerobic ecosystem may have played in the Archean Earth is discussed.

California↗