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Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold 2019 University of Massachusetts Amherst

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to temperature and ...


Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger 2019 Marshall University

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit ...


Heterologous Expression Of Secreted Bacterial Bpp And Hap Phytases In Plants Stimulates Arabidopsis Thaliana Growth On Phytate., Lia R. Valeeva, Chuluuntsetseg Nyamsuren, Margarita R. Sharipova, Eugene V. Shakirov 2019 Marshall University

Heterologous Expression Of Secreted Bacterial Bpp And Hap Phytases In Plants Stimulates Arabidopsis Thaliana Growth On Phytate., Lia R. Valeeva, Chuluuntsetseg Nyamsuren, Margarita R. Sharipova, Eugene V. Shakirov

Yevgeniy (Eugene) Shakirov

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family ...


Identifiying High Risk Areas Of Zika Virus Infection By Meteorological Factors In Columbia, Lung-Chang Chien, Francisco Sy, Adriana Perez 2019 University of Nevada, Las Vegas

Identifiying High Risk Areas Of Zika Virus Infection By Meteorological Factors In Columbia, Lung-Chang Chien, Francisco Sy, Adriana Perez

Environmental & Occupational Health Faculty Publications

Background Several Zika virus (ZIKV) outbreaks have occurred since October 2015. Because there is no effective treatment for ZIKV infection, developing an effective surveillance and warning system is currently a high priority to prevent ZIKV infection. Despite Aedes mosquitos having been known to spread ZIKV, the calculation approach is diverse, and only applied to local areas. This study used meteorological measurements to monitor ZIKV infection due to the high correlation between climate change and Aedes mosquitos and the convenience to obtain meteorological data from weather monitoring stations. Methods This study applied the Bayesian structured additive regression modeling approach to include ...


Insights Into The Ecological Roles And Evolution Of Methyl-Coenzyme M Reductase-Containing Hot Spring Archaea, Zheng-Shuang Hua, Yu-Lin Wang, Paul N. Evans, Yan-Ni Qu, Kian Mau Goh, Yang-Zhi Rao, Sun Yat-Sen University Qi, Yu-Xian Li, Min-Jun Huang, Jian-Yu Jiao, Ya-Ting Chen, Wen-Sheng Shu, Wael Hozzein, Brian P. Hedlund, Gene W. Tyson, Tong Zhang, Wen-Jun Li 2019 Sun Yat-Sen University

Insights Into The Ecological Roles And Evolution Of Methyl-Coenzyme M Reductase-Containing Hot Spring Archaea, Zheng-Shuang Hua, Yu-Lin Wang, Paul N. Evans, Yan-Ni Qu, Kian Mau Goh, Yang-Zhi Rao, Sun Yat-Sen University Qi, Yu-Xian Li, Min-Jun Huang, Jian-Yu Jiao, Ya-Ting Chen, Wen-Sheng Shu, Wael Hozzein, Brian P. Hedlund, Gene W. Tyson, Tong Zhang, Wen-Jun Li

Life Sciences Faculty Publications

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens ...


Simulating Bacterial Growth, Competition, And Resistance With Agent-Based Models And Laboratory Experiments, Anne E. Yust, Davida S. Smyth 2019 The New School

Simulating Bacterial Growth, Competition, And Resistance With Agent-Based Models And Laboratory Experiments, Anne E. Yust, Davida S. Smyth

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Reproduction And Dispersal Of Biological Soil Crust Organisms, Steven D. Warren, Larry L. St. Clair, Lloyd R. Stark, Louise A. Lewis, Nuttapon Pombubpa, Tania Kurbessoian, Jason E. Stajich, Zachary T. Aanderud 2019 U.S. Forest Service

Reproduction And Dispersal Of Biological Soil Crust Organisms, Steven D. Warren, Larry L. St. Clair, Lloyd R. Stark, Louise A. Lewis, Nuttapon Pombubpa, Tania Kurbessoian, Jason E. Stajich, Zachary T. Aanderud

Life Sciences Faculty Publications

Biological soil crusts (BSCs) consist of a diverse and highly integrated community of organisms that effectively colonize and collectively stabilize soil surfaces. BSCs vary in terms of soil chemistry and texture as well as the environmental parameters that combine to support unique combinations of organisms—including cyanobacteria dominated, lichen-dominated, and bryophyte-dominated crusts. The list of organismal groups that make up BSC communities in various and unique combinations include—free living, lichenized, and mycorrhizal fungi, chemoheterotrophic bacteria, cyanobacteria, diazotrophic bacteria and archaea, eukaryotic algae, and bryophytes. The various BSC organismal groups demonstrate several common characteristics including—desiccation and extreme temperature tolerance ...


What About The Environment?: Exploring The Neglected Third Dimension Of Antimicrobial Resistance, Paige E. Montfort 2019 SIT Study Abroad

What About The Environment?: Exploring The Neglected Third Dimension Of Antimicrobial Resistance, Paige E. Montfort

Independent Study Project (ISP) Collection

Antimicrobial resistance (AMR) is one of the most urgent and complex health risks of our time, with links to human health, animal health, and the environment. The majority of research and policy related to AMR, however, has been dedicated to human and animal health. The third dimension — the environment — has been relatively neglected. Conversations about this problem have begun, but gaps in understanding remain. This study explores the key barriers that have hindered developments related to the environmental aspect of AMR and some of the solutions that have begun to or could be utilized to overcome these barriers.

A grounded ...


Inhibitors Of Eicosanoid Biosynthesis Reveal That Multiple Lipid Signaling Pathways Influence Malaria Parasite Survival In Anopheles Gambiae, Hyeogsun Kwon, Ryan C. Smith 2019 Iowa State University

Inhibitors Of Eicosanoid Biosynthesis Reveal That Multiple Lipid Signaling Pathways Influence Malaria Parasite Survival In Anopheles Gambiae, Hyeogsun Kwon, Ryan C. Smith

Entomology Publications

Eicosanoids are bioactive signaling lipids derived from the oxidation of fatty acids that act as important regulators of immune homeostasis and inflammation. As a result, effective anti-inflammatory drugs have been widely used to reduce pain and inflammation which target key eicosanoid biosynthesis enzymes. Conserved from vertebrates to insects, the use of these eicosanoid pathway inhibitors offer opportunities to evaluate the roles of eicosanoids in less-characterized insect systems. In this study, we examine the potential roles of eicosanoids on malaria parasite survival in the mosquito Anopheles gambiae. Using Plasmodium oocyst numbers to evaluate parasite infection, general or specific inhibitors of eicosanoid ...


Tungsten Is Essential For Long-Term Maintenance Of Members Of Candidate Archaeal Genus Aigarchaeota Group 4, Joshua Robert Reyes Dimapilis 2019 California State University - San Bernardino

Tungsten Is Essential For Long-Term Maintenance Of Members Of Candidate Archaeal Genus Aigarchaeota Group 4, Joshua Robert Reyes Dimapilis

Electronic Theses, Projects, and Dissertations

Aigarchaeota, a deeply branching archaeal lineage with no cultivated representatives, is found in geothermal and hydrothermal systems worldwide and consists of at least 9 genus-level groups, each predicted to have diverse metabolic capabilities. This candidate archaeal phylum is part of the TACK superphylum, members of which possess eukaryotic-signature proteins, thus suggesting that they may represent evolutionary steps along the way to the genesis of the first eukaryotic cells. Cultivating members of Aigarchaeota would elucidate how eukaryotes arose in evolutionary history and provide biotechnological applications. Aigarchaeota Group 4 (AigG4), one genus in Aigarchaeota, was previously found to be abundant in corn ...


Using Single-Cell Sorting, Fish And 13c-Labeling To Cultivate And Assess Carbon Substrate Utilization Of ‘Aigarchaeota’ And Other Novel Thermophiles, Damon Kurtis Mosier 2019 California State University, San Bernardino

Using Single-Cell Sorting, Fish And 13c-Labeling To Cultivate And Assess Carbon Substrate Utilization Of ‘Aigarchaeota’ And Other Novel Thermophiles, Damon Kurtis Mosier

Electronic Theses, Projects, and Dissertations

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was ...


Isolation Of Caldatribacterium (Op9) And Investigation Of Its Potential Interactions With A Novel, Co-Cultivated Thermodesulfobacterium Species, Toshio Alvarado 2019 California State University, San Bernardino

Isolation Of Caldatribacterium (Op9) And Investigation Of Its Potential Interactions With A Novel, Co-Cultivated Thermodesulfobacterium Species, Toshio Alvarado

Electronic Theses, Projects, and Dissertations

Atribacteria (OP9), candidate phylum with no representatives in pure culture, is found in various anaerobic environments worldwide. “Caldatribacterium”, a lineage within Atribacteria that is predicted to be a strictly anaerobic sugar fermenter based on cultivation-independent genomic analyses, is currently being maintained in lab enrichment cultures with fucose as its sole growth substrate. Metagenomics and 16S rRNA gene tag sequencing indicated that the fucose culture was a co-culture of “Caldatribacterium” and an uncultivated member of the genus Thermodesulfobacterium. Due to failed attempts to isolate “Caldatribacterium” by dilution-to-extinction and plating, it was hypothesized that “Caldatribacterium” is dependent in some way on the ...


Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. MacDonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner 2019 Leiden University

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Andrew Ozga

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon ...


Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner 2019 Max Planck Institute for the Science of Human History; University of Oklahoma

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Andrew Ozga

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is ...


Are Microclimate Conditions In El Malpais National Monument Caves In New Mexico, Usa Suitable For Pseudogymnoascus Growth?, Terry J. Torres-Cruz, Andrea Porras-Alfaro, Nicole A. Caimi, Ogochukwu Nwabologu, Edward W. Strach, Kaitlyn J.H. Read, Jesse M. Young, Debbie C. Buecher, Diana E. Northup 2019 Western Illinois University

Are Microclimate Conditions In El Malpais National Monument Caves In New Mexico, Usa Suitable For Pseudogymnoascus Growth?, Terry J. Torres-Cruz, Andrea Porras-Alfaro, Nicole A. Caimi, Ogochukwu Nwabologu, Edward W. Strach, Kaitlyn J.H. Read, Jesse M. Young, Debbie C. Buecher, Diana E. Northup

International Journal of Speleology

White-nose syndrome (WNS) is a bat disease caused by the fungal pathogen Pseudogymnoascus destructans, which thrives in cold and very humid environments where bats frequently hibernate. Conidia of Pseudogymnoascus species are often documented on bats prior to the onset of WNS, but characterization of high-risk areas defined by microclimate cave conditions have been lacking. Investigating the occurrence of this fungal genus and appropriate environmental conditions to support P. destructans in southwestern U.S. caves is key to understanding the sites most likely to be impacted by WNS. Microclimate conditions in ten caves at El Malpais (ELMA) National Monument in New ...


Glycolic Acid Utilization In Two Species Of Marine Bacteria, Erik S. Timsak 2019 California Polytechnic State University, San Luis Obispo

Glycolic Acid Utilization In Two Species Of Marine Bacteria, Erik S. Timsak

STAR Program Research Presentations

Interactions between bacteria and phytoplankton are crucial for the cycling of organic matter in marine environments. Around 50% of organic carbon taken up by marine bacteria is converted into inorganic carbon. The uptake of organic carbon by marine bacteria exuded from phytoplankton is a key factor in regulating the marine carbon cycle. One such molecule that is exuded by phytoplankton and then uptaken by marine bacteria is called glycolate - the anion of glycolic acid, a two caron molecule. Glycolate is exuded by phytoplankton during photorespiration and 10-50% of dissolved organic carbon in marine environments is comprised of glycolate. Additionally, production ...


16s Rrna Analysis And Toxin Gene Presence In Escherichia Coli Isolated From Beach Water And Sand At A Public Beach (Erie County, Ny), Jennifer D. Jackson 2019 State University of New York College at Buffalo - Buffalo State College

16s Rrna Analysis And Toxin Gene Presence In Escherichia Coli Isolated From Beach Water And Sand At A Public Beach (Erie County, Ny), Jennifer D. Jackson

Biology Theses

Every year, thousands of people utilize beaches for recreation, but most are unaware of Escherichia coli (E. coli) contamination and the possibility of acquiring an infection. In this study, 173 strains of E. coli were isolated from sand and adjacent waters from a public beach in Erie County, NY and analyzed for genetic relatedness based on sequence differences in the variable regions of the 16S rRNA gene. Some of the variable regions (V1 and V6) proved useful in constructing phylogenetic trees but the discriminatory power of these regions was inadequate to resolve intraspecies differences. Therefore, whether extant populations of E ...


Urban Grassland Management Implications For Soil C And N Dynamics: A Microbial Perspective, Grant L. Thompson, Jenny Kao-Kniffin 2019 Iowa State University

Urban Grassland Management Implications For Soil C And N Dynamics: A Microbial Perspective, Grant L. Thompson, Jenny Kao-Kniffin

Horticulture Publications

Urban grasslands are turfgrass dominated landscapes of varying functions and uses that are ubiquitous in areas associated with human population growth and urbanization. While these landscapes are perceived to serve a primarily aesthetic function, they provide a multitude of beneficial ecosystem functions that impervious surfaces do not provide. Urban grassland soils have been shown to accumulate carbon (C) and nitrogen (N) for decades, matching native grasslands and eastern hardwood forest soils in terms of C and N densities. The establishment and maintenance of urban grasslands alters many microbially-mediated biogeochemical processes in soils, including soil organic matter (SOM) dynamics. Despite strong ...


Microbiota Of Newborn Calves And Their Mothers Reveals Possible Transfer Routes For Newborn Calves’ Gastrointestinal Microbiota, Daniela Klein-Jöbstl, Narciso M. Quijada, Monika Dzieciol, Benjamin Feldbacher, Matrin Wagner, Marc Drillich, Stephan Schmitz-Esser, Evelyne Mann 2019 University of Veterinary Medicine Vienna

Microbiota Of Newborn Calves And Their Mothers Reveals Possible Transfer Routes For Newborn Calves’ Gastrointestinal Microbiota, Daniela Klein-Jöbstl, Narciso M. Quijada, Monika Dzieciol, Benjamin Feldbacher, Matrin Wagner, Marc Drillich, Stephan Schmitz-Esser, Evelyne Mann

Animal Science Publications

The intestinal microbiota of newborns plays an important role in the development of immunity and metabolism. In livestock animals, knowledge of the intestinal microbiota is essential not only to prevent diseases but also to optimize weight gain and performance. The aim of our study was to examine faecal samples repeatedly within the first two days of life using 16S rRNA gene High Throughput Sequencing. Additionally, samples from the mouths of the calves and the vaginas, colostrum, and faeces of the dams were included to evaluate possible sources of the calf faecal microbiota. The calf faecal microbiota was highly variable during ...


Characterizing Nodule Endophyte Communities In Glycine Max And Lablab Purpureus Using Next-Generation Sequencing, Scott David McElveen 2019 Missouri State University

Characterizing Nodule Endophyte Communities In Glycine Max And Lablab Purpureus Using Next-Generation Sequencing, Scott David Mcelveen

MSU Graduate Theses

Biological nitrogen fixation by rhizobia in the root nodules of legumes is a significant source of agricultural nitrogen in global crop production systems. The influence of and interaction of factors involved in nodule endophyte selection remain poorly understood. In the present study, the influences of crop rotation (soybean-legume vs. cotton-legume) and recalcitrant soil organic matter (compost amendment) on the relative distribution of endophytic bacteria in the root nodules of greenhouse-grown soybean and lablab were investigated by extracting, amplifying, and sequencing 16S ribosomal RNA (rRNA) and nifH genes. Neither preceding crop nor compost amendment were found to have an influence on ...


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