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Articles 1 - 19 of 19

Full-Text Articles in Life Sciences

Changes In Microbial Communities Along Redox Gradients In Polygonized Arctic Wet Tundra Soils, David A. Lipson, Ted K. Raab, Melanie Parker, Scott T. Kelley, Colin J. Brislawn, Janet Jansson Jun 2015

Changes In Microbial Communities Along Redox Gradients In Polygonized Arctic Wet Tundra Soils, David A. Lipson, Ted K. Raab, Melanie Parker, Scott T. Kelley, Colin J. Brislawn, Janet Jansson

Ted K. Raab

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska, and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were ...


Selection And Phenotypic Characterization Of A Core Collection Of Brachypodium Distachyon Inbred Lines, Ludmilla Tyler, Johnathan U. Fangel, Alexandra D. Fagerström, Michael A. Steinwand, Ted K. Raab, William Gt Willats, John P. Vogel Jan 2014

Selection And Phenotypic Characterization Of A Core Collection Of Brachypodium Distachyon Inbred Lines, Ludmilla Tyler, Johnathan U. Fangel, Alexandra D. Fagerström, Michael A. Steinwand, Ted K. Raab, William Gt Willats, John P. Vogel

Ted K. Raab

The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height ...


Water Stress Strengthens Mutualism Among Ants, Trees, And Scale Insects, Elizabeth G. Pringle, Erol Akc¸Ay, Ted K. Raab, Rodolfo Dirzo, Deborah M. Gordon Nov 2013

Water Stress Strengthens Mutualism Among Ants, Trees, And Scale Insects, Elizabeth G. Pringle, Erol Akc¸Ay, Ted K. Raab, Rodolfo Dirzo, Deborah M. Gordon

Ted K. Raab

Abiotic environmental variables strongly affect the outcomes of species interactions. For example, mutualistic interactions between species are often stronger when resources are limited. The effect might be indirect: water stress on plants can lead to carbon stress, which could alter carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses, plants host ant colonies that defend them against herbivores. Here we show that the partners’ investments in a widespread ant–plant symbiosis increase with water stress across 26 sites along a Mesoamerican precipitation gradient. At lower precipitation levels, Cordia alliodora trees invest more carbon in Azteca ants via phloem-feeding scale insects that ...


The Contribution Of Fe (Iii) And Humic Acid Reduction To Ecosystem Respiration In Drained Thaw Lake Basins Of The Arctic Coastal Plain, David A. Lipson, Ted K. Raab, Dominic Goria, Jaime Zlamal May 2013

The Contribution Of Fe (Iii) And Humic Acid Reduction To Ecosystem Respiration In Drained Thaw Lake Basins Of The Arctic Coastal Plain, David A. Lipson, Ted K. Raab, Dominic Goria, Jaime Zlamal

Ted K. Raab

Previous research showed that anaerobic respiration using iron (Fe) oxides as terminal electron acceptor contributed substantially to ecosystem respiration (ER) in a drained thaw lake basin (DTLB) on the Arctic coastal plain. As DTLB age, the surface organic layer thickens, progressively burying the Fe-rich mineral layers. We therefore hypothesized that Fe (III) availability and Fe reduction would decline with basin age. We studied four DTLB across an age gradient, comparing seasonal changes in the oxidation state of dissolved and extractable Fe pools and the estimated contribution of Fe reduction to ER. The organic layer thickness did not strictly increase with ...


Metagenomic Insights Into Anaerobic Metabolism Along An Arctic Peat Soil Profile, David A. Lipson, John M. Haggerty, Archana Srinivas, Ted K. Raab, Shashank Sathe, Elizabeth A. Dinsdale May 2013

Metagenomic Insights Into Anaerobic Metabolism Along An Arctic Peat Soil Profile, David A. Lipson, John M. Haggerty, Archana Srinivas, Ted K. Raab, Shashank Sathe, Elizabeth A. Dinsdale

Ted K. Raab

A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance ...


Evidence That Glucose Is The Major Transferred Metabolite In Dinoflagellate–Cnidarian Symbiosis, Matthew S. Burriesci, Ted K. Raab, John R. Pringle Oct 2012

Evidence That Glucose Is The Major Transferred Metabolite In Dinoflagellate–Cnidarian Symbiosis, Matthew S. Burriesci, Ted K. Raab, John R. Pringle

Ted K. Raab

Reef-building corals and many other cnidarians are symbiotic with dinoflagellates of the genus Symbiodinium. It has long been known that the endosymbiotic algae transfer much of their photosynthetically fixed carbon to the host and that this can provide much of the hostʼs total energy. However, it has remained unclear which metabolite(s) are directly translocated from the algae into the host tissue. We reexamined this question in the small sea anemone Aiptasia using labeling of intact animals in the light with 13C-bicarbonate, rapid homogenization and separation of animal and algal fractions, and analysis of metabolite labeling by gas chromatography-mass spectrometry ...


Water Table Height And Microtopography Control Biogeochemical Cycling In An Arctic Coastal Tundra Ecosystem, David A. Lipson, Donatella Zona, Ted K. Raab, Francis Bozzolo, Marguerite Mauritz, Walter C. Oechel Jan 2012

Water Table Height And Microtopography Control Biogeochemical Cycling In An Arctic Coastal Tundra Ecosystem, David A. Lipson, Donatella Zona, Ted K. Raab, Francis Bozzolo, Marguerite Mauritz, Walter C. Oechel

Ted K. Raab

Drained thaw lake basins (DTLB’s) are the dominant land form of the Arctic Coastal Plain in northern Alaska. The presence of continuous permafrost prevents drainage and so water tables generally remain close to the soil surface, creating saturated, suboxic soil conditions. However, ice wedge polygons produce microtopographic variation in these landscapes, with raised areas such as polygon rims creating more oxic microenvironments. The peat soils in this ecosystem store large amounts of organic carbon which is vulnerable to loss as arctic regions continue to rapidly warm, and so there is great motivation to understand the controls over microbial activity ...


Reduction Of Iron (Iii) And Humic Substances Plays A Major Role In Anaerobic Respiration In An Arctic Peat Soil, David A. Lipson, Mony Jha, Ted K. Raab, Walter C. Oechel Dec 2010

Reduction Of Iron (Iii) And Humic Substances Plays A Major Role In Anaerobic Respiration In An Arctic Peat Soil, David A. Lipson, Mony Jha, Ted K. Raab, Walter C. Oechel

Ted K. Raab

Arctic peat soils contain vast reserves of organic C and are largely anaerobic. However, anaerobic respiration, particularly the role of Fe(III) and humic substances as electron acceptors, is not well understood in such ecosystems. We investigated these processes in a drained thaw lake basin on the Arctic coastal plain near Barrow, Alaska. We measured concentrations of soluble Fe and other potential electron acceptors, described the microbial community, and performed experiments in the laboratory and field to measure net rates of Fe(III) reduction and the relationship of this process to C cycling. In most areas within the basin, aerobic ...


The Coconut Palm, Cocos Nucifera, Impacts Forest Composition And Soil Characteristics At Palmyra Atoll, Central Pacific, Hillary S. Young, Ted K. Raab, Douglas J. Mccauley, Amy A. Briggs, Rodolfo Dirzo Jan 2010

The Coconut Palm, Cocos Nucifera, Impacts Forest Composition And Soil Characteristics At Palmyra Atoll, Central Pacific, Hillary S. Young, Ted K. Raab, Douglas J. Mccauley, Amy A. Briggs, Rodolfo Dirzo

Ted K. Raab

Cocos nucifera, the coconut palm, has a pantropical distribution and reaches near monodominance in many atolls, low lying islands and coastal regions. This paper examines the ecological correlation between C. nucifera abundance and changes in forest structure, floristic diversity and forest soil characteristics. Cumulatively, these data show that C. nucifera has important impacts on floristic, structural and soil characteristics of forests where it becomes dominant. Given the high proportion of tropical coastal areas in which C. nucifera is now naturalized and abundant, this likely has important implications for coastal forest diversity and structure.


Towards A Systems Approach To Understanding Plant Cell Walls, Chris R. Somerville, Stefan Bauer, Ginger Brininstool, Michelle Facette, Thorsten Hamann, Jennifer Milne, Erin Osborne, Alex Paradez, Staffan Persson, Ted K. Raab, Sonja Vorwerk, Heather Youngs Dec 2004

Towards A Systems Approach To Understanding Plant Cell Walls, Chris R. Somerville, Stefan Bauer, Ginger Brininstool, Michelle Facette, Thorsten Hamann, Jennifer Milne, Erin Osborne, Alex Paradez, Staffan Persson, Ted K. Raab, Sonja Vorwerk, Heather Youngs

Ted K. Raab

One of the defining features of plants is a body plan based on the physical properties of cell walls. Structural analyses of the polysaccharide components, combined with highresolution imaging, have provided the basis for much of the current understanding of cell walls. The application of genetic methods has begun to provide new insights into how walls are made, how they are controlled, and how they function. However, progress in integrating biophysical, developmental, and genetic information into a useful model will require a system-based approach.


Mutations In Pmr5 Result In Powdery Mildew Resistance And Altered Cell Wall Composition, John P. Vogel, Ted K. Raab, Chris R. Somerville, Shauna C. Somerville Dec 2004

Mutations In Pmr5 Result In Powdery Mildew Resistance And Altered Cell Wall Composition, John P. Vogel, Ted K. Raab, Chris R. Somerville, Shauna C. Somerville

Ted K. Raab

Powdery mildews and other obligate biotrophic pathogens are highly adapted to their hosts and often show limited host ranges. One facet of such host specialization is likely to be penetration of the host cell wall, a major barrier to infection. A mutation in the pmr5 gene rendered Arabidopsis resistant to the powdery mildew species Erysiphe cichoracearum and Erysiphe orontii, but not to the unrelated pathogens Pseudomonas syringae or Peronospora parasitica. PMR5 belongs to a large family of plant-specific genes of unknown function. pmr5-mediated resistance did not require signaling through either the salicylic acid or jasmonic acid/ ethylene defense pathways, suggesting ...


Ecological And Agricultural Applications Of Synchrotron Ir Microscopy, Ted K. Raab, John P. Vogel Sep 2004

Ecological And Agricultural Applications Of Synchrotron Ir Microscopy, Ted K. Raab, John P. Vogel

Ted K. Raab

The diffraction-limited spot size of synchrotron-based IR microscopes provides cell-specific, spectrochemical imaging of cleared leaf, stem and root tissues of the model genetic organism Arabidopsis thaliana, and mutant plants created either by T-DNA insertional inactivation or chemical mutagenesis. Spectra in the wavelength region from 6 to 12 microns provide chemical and physical information on the cell wall polysaccharides of mutants lacking particular biosynthetic enzymes (‘‘Cellulose synthase-like’’ genes). In parallel experiments, synchrotron IR microscopy delineates the role of Arabidopsis cell wall enzymes as susceptibility factors to the fungus Erysiphe cichoracearum, a causative agent of powdery mildew disease. Three genes, pmr4, pmr5 ...


Pmr6, A Pectate Lyase–Like Gene Required For Powdery Mildew Susceptibility In Arabidopsis, John P. Vogel, Ted K. Raab, Celine Schiff, Shauna C. Somerville Sep 2002

Pmr6, A Pectate Lyase–Like Gene Required For Powdery Mildew Susceptibility In Arabidopsis, John P. Vogel, Ted K. Raab, Celine Schiff, Shauna C. Somerville

Ted K. Raab

The plant genes required for the growth and reproduction of plant pathogens are largely unknown. In an effort to identify these genes, we isolated Arabidopsis mutants that do not support the normal growth of the powdery mildew pathogen Erysiphe cichoracearum. Here, we report on the cloning and characterization of one of these genes, PMR6. PMR6 encodes a pectate lyase-like protein with a novel C-terminal domain. Consistent with its predicted gene function, mutations in PMR6 alter the composition of the plant cell wall, as shown by Fourier transform infrared spectroscopy. pmr6-mediated resistance requires neither salicylic acid nor the ability to perceive ...


Visualizing Rhizosphere Chemistry Of Legumes With Mid-Infrared Synchrotron Radiation, Ted K. Raab, Michael C. Martin May 2001

Visualizing Rhizosphere Chemistry Of Legumes With Mid-Infrared Synchrotron Radiation, Ted K. Raab, Michael C. Martin

Ted K. Raab

A bright synchrotron light source operated by the Lawrence Berkeley National Laboratory served as an external source for infrared (IR) microscopy of plant root microcosms. Mid-IR light from synchrotrons is 2-3 orders of magnitude brighter than conventional sources, providing contrast based on the chemical information in the reflected signal at a spatial resolution near the diffraction-limit of 3-10 microns. In an experiment using plant root microcosms fitted with zinc selenide IR-transmissive windows (50 mm x 20 mm x 1 mm), we describe chemical differences and similarities within the root zone of mung bean (Vigna radiata L.), grown with or without ...


Effects Of Willows (Salix Brachycarpa) On Populations Of Salicylate-Mineralizing Microorganisms In Alpine Soils, Steven K. Schmidt, David A. Lipson, Ted K. Raab Sep 2000

Effects Of Willows (Salix Brachycarpa) On Populations Of Salicylate-Mineralizing Microorganisms In Alpine Soils, Steven K. Schmidt, David A. Lipson, Ted K. Raab

Ted K. Raab

We used the substrate-induced growth-response (SIGR) method to quantify salicylate-mineralizing microbes and total microbial biomass in soils from under willows (Salix brachycarpa) and in surrounding meadows dominated by the sedge Kobresia myosuroides. Willows had a strong effect on the biomass of salicylate-mineralizing microbes in both years of this study. There were always higher biomass levels of salicylate mineralizers in soils from under Salix (4.6–10.1 ug C/ g) than under Kobresia (0.23–0.76 ug/ g). In contrast, total microbial biomass was not significantly different under these plant species in 1996 and was only higher under Salix ...


Toward An Ecosystem Approach To Remediation In The Great Basin, Ted K. Raab Jan 2000

Toward An Ecosystem Approach To Remediation In The Great Basin, Ted K. Raab

Ted K. Raab

We consider the web of interactions among geologic materials, soils, plants, and animals to ask, "If mining or other extractive energy technologies occur in desert regions, what do we need to know to return the land to productivity?" The Great Basin represents a formidable challenge in this regard, as winters in these cold deserts and seasonal lack of moisture during parts of the year severely constrain the growing season for vegetation. Due to the nature of current or proposed mining activities in this region, we have chosen to concentrate on two potential pollutants: the trace element selenium (Se) and nitrate ...


Soil Amino Acid Utilization Among Species Of The Cyperaceae: Plant And Soil Processes, Ted K. Raab, David A. Lipson, Steven K. Scmidt, Russ K. Monson Jan 1999

Soil Amino Acid Utilization Among Species Of The Cyperaceae: Plant And Soil Processes, Ted K. Raab, David A. Lipson, Steven K. Scmidt, Russ K. Monson

Ted K. Raab

Amino acids are released during the decomposition of soil organic matter and have been shown to be utilized as a nitrogen source by some non-mycorrhizal species in the family Cyperaceae (the sedge family). Twelve out of 13 Cyperaceae species examined in the current study were capable of absorbing soil amino acids in the non-mycorrhizal state. With two exceptions (two species in the genus Kobresia), species from subalpine or alpine habitats exhibited lower rates of total nitrogen uptake compared to species from more temperate habitats, which is possibly explained by lower growth rates in the alpine and subalpine species and a ...


Variation In Competitive Abilities Of Plants And Microbes For Specific Amino Acids, David A. Lipson, Ted K. Raab, Steven K. Schmidt, Russ K. Monson Jan 1999

Variation In Competitive Abilities Of Plants And Microbes For Specific Amino Acids, David A. Lipson, Ted K. Raab, Steven K. Schmidt, Russ K. Monson

Ted K. Raab

Microbes are assumed to possess strong competitive advantages over plants for uptake of nutrients from the soil. The finding that non-mycorrhizal plants can obtain a significant fraction of their N requirement from soil amino acids contradicts this assumption. The amino acid glycine (Gly) has been used as a model amino acid in many recent studies. Our preliminary studies showed that Gly was a poor substrate for microbial growth compared to other amino acids. We tested the hypothesis that the alpine sedge Kobresia myosuroides competes better for Gly than for other amino acids because of decreased microbial demand for this compound ...


Non-Mycorrhizal Uptake Of Amino Acids By Roots Of The Alpine Sedge Kobresia Myosuroides: Implications For The Alpine Nitrogen Cycle, Ted K. Raab, David A. Lipson, Russ K. Monson Jan 1996

Non-Mycorrhizal Uptake Of Amino Acids By Roots Of The Alpine Sedge Kobresia Myosuroides: Implications For The Alpine Nitrogen Cycle, Ted K. Raab, David A. Lipson, Russ K. Monson

Ted K. Raab

Non-mycorrhizal plants of the alpine sedge, Kobresia myosuroides , take up the amino acid glycine from nutrient solutions at greater rates than NO3- or NH4+. The amino acids glutamate and proline were also taken up at high rates. Total plant biomass was twice as high after 4 months of growth on glycine, compared to NH4NO3, with significant increases in both root and leaf biomass. By taking advantage of differences in the d13C signature of air in the growth chamber and the glycine used for growth, a two-member mixing model was used to estimate that a significant amount of the glycine was ...