Environmental Microbiology and Microbial Ecology Commons^™

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 drought-responsive G×E. …

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 …

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

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 …

Flow Cytometric Analysis Of Freshwater Cyanobacteria: A Case Study, Tin-Chun Chu, Ruchit Patel, Aline De Oliveira, Robert Newby Jr

Tinchun Chu, Ph.D.

No abstract provided.

Comparison Study Of The Averaged Sediment Microbial Enzyme Activities In Four Fecally-Contaminated Streams In The Same Watershed In Northeast Tennessee To Biochemical Oxygen Demand, Nitrate Concentration, And Phosphate Concentration, Brian G. Evanshen, Kurt J. Maier, Phillip R. Scheuerman

Phillip R. Scheuerman

Microbial enzyme activities (MEA’s) are measurements of microbial metabolism. These activities are dependent on the need for nutrients and respiration. This extended study evaluated four streams in the same watershed that had an approved fecal coliform Total Maximum Daily Load. Sediment and water samples were collected monthly for the first year of each specific stream study, and then quarterly to the end of 2006. Dehydrogenase, a measure of microbial respiration, along with acid phosphatase, alkaline phosphatase, galactosidase and glucosidase activities were measured using colorimetric assays. Biochemical oxygen demand (BOD) was determined using the standard 5-day test (BOD₅). Nitrate …

Comparison Of Microbial Water Quality Parameters Of Four Geographically Similar Creeks In Northeast Tennessee, Kimberlee K. Hall, L. K. Gallagher, Brian G. Evanshen, Kurt J. Maier, Phillip R. Scheuerman

Phillip R. Scheuerman

Four creeks within the Watauga River watershed in Northeast Tennessee are routinely monitored for water quality assessments. To identify sources and monitor remediation, Sinking Creek, Cash Hollow Creek, Buffalo Creek and Boones Creek are monitored for chemical and microbial parameters. These parameters include phosphates, nitrates, BOD and fecal coliforms. Sinking Creek is a tributary of the Watauga River with 10 miles of impaired water. Cash Hollow Creek enters the Watauga River at river mile 11.4 with 3.4 miles of impaired water. Boones Creek contains 18.6 impaired miles while the status of water quality in Buffalo Creek is not yet determined. …

Comparison Study Of Sediment Microbial Enzyme Activities To Biochemical Oxygen Demand, Nitrate Concentration, Phosphate Concentration In The Sediments Of A Fecally-Contaminated Stream In Northeast Tennessee Relative To Season And Land Use, Brian G. Evanshen, Kurt J. Maier, Phillip R. Scheuerman

Phillip R. Scheuerman

Microbial metabolism reacts quickly to environmental conditions. These reactions are dependent on the need for nutrients and respiration and can be measured using an assay of individual microbial enzyme activities (MEA’s). In this study, we measured MEA’s in the sediments of a stream in northeast Tennessee that had an approved fecal coliform Total Maximum Daily Load (TMDL). These values were compared to biochemical oxygen demand (BOD), phosphate concentration and nitrate concentration in the water column of this stream. Comparisons were grouped by season and land use. Stream sediments and water were collected monthly for one year and then quarterly for …

18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti

Catherine Putonti

Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Catherine Putonti

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …

Freshwater Fungal Infections, Dennis J. Baumgardner

Dennis J. Baumgardner, MD

Fungal infections as a result of freshwater exposure or trauma are fortunately rare. Etiologic agents are varied, but commonly include filamentous fungi and Candida. This narrative review describes various sources of potential freshwater fungal exposure and the diseases that may result, including fungal keratitis, acute otitis externa and tinea pedis, as well as rare deep soft tissue or bone infections and pulmonary or central nervous system infections following traumatic freshwater exposure during natural disasters or near-drowning episodes. Fungal etiology should be suspected in appropriate scenarios when bacterial cultures or molecular tests are normal or when the infection worsens or fails …

In Vitro Studies On Metabolism Of Salvinorin A, Lukasz M. Kutrzeba, Vardan T. Karamyan, Robert C. Speth, John S. Williamson, Jordan K. Zjawiony

John S. Williamson

Microbial transformation of natural products is a well established model for mammalian metabolism. Salvinorin A, a diterpenoid isolated from the hallucinogenic mint Salvia divinorum Epling & Játiva-M (Lamiaceae), is a potent non-nitrogenous κ-opioid receptor agonist. The metabolism of salvinorin A has still not yet been well established. Thirty fungal species were screened for the ability to metabolize salvinorin A. We observed that salvinorin A undergoes fast hydrolysis of the acetate group at carbon atom C2, resulting in formation of the pharmacologically inactive product, salvinorin B. Ex vivo experiments were also performed using organelle fractions isolated from rat liver and brain. …

Genomic Plasticity And Rapid Host Switching Can Promote The Evolution Of Generalism: A Case Study In The Zoonotic Pathogen Campylobacter, Dan J. Woodcock, Peter Krusche, Norval J. C. Strachan, Ken J. Forbes, Frederick M. Cohan, Guillaume Meric, Samuel K. Sheppard

Frederick M. Cohan

Disease-Causing Fungi In Homes And Yards In The Midwestern United States, Dennis J. Baumgardner

Dennis J. Baumgardner, MD

A number of fungal pathogens that may result in a variety of human diseases are found in residential homes and yards. The growth of these microscopic fungi is often favored by particular characteristics of the dwelling and nearby outdoor environment. Evolved virulence factors or increased ability of specific fungi to grow in diverse, and sometimes harsh, microenvironments presented by the domestic environment may promote growth and pathogenesis. Infection may occur by inhalation or direct inoculation and include endemic fungi in addition to opportunistic or emerging species. Systemic or locally aggressive fungal infections are particularly likely and may be life-threatening in …

Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li

Frank S. Gilliam

Improved management of soil carbon (C) and nitrogen (N) storage in agro-ecosystems represents an important strategy for ensuring food security and sustainable agricultural development in China. Accurate estimates of the distribution of soil C and N stores and their relationship to crop yield are crucial to developing appropriate cropland management policies. The current study examined the spatial variation of soil organic C (SOC), total soil N (TSN), and associated variables in the surface layer (0–40 cm) of soils from intensive agricultural systems in 19 counties within Henan Province, China, and compared these patterns with crop yield. Mean soil C and …

Nutrient Limitation In Three Lowland Tropical Forests In Southern China Receiving High Nitrogen Deposition: Insights From Fine Root Responses To Nutrient Additions, Feifei Zhu, Muneoki Yoh, Frank S. Gilliam, Xiankai Lu, Jiangming Mo

Frank S. Gilliam

Elevated nitrogen (N) deposition to tropical forests may accelerate ecosystem phosphorus (P) limitation. This study examined responses of fine root biomass, nutrient concentrations, and acid phosphatase activity (APA) of bulk soil to five years of N and P additions in one old-growth and two younger lowland tropical forests in southern China. The old-growth forest had higher N capital than the two younger forests from long-term N accumulation. From February 2007 to July 2012, four experimental treatments were established at the following levels: Control, N-addition (150 kg N ha–1 yr–1), P-addition (150 kg P ha–1 yr–1) and N+P-addition (150 kg N …

Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li

Frank S. Gilliam

Improved management of soil carbon (C) and nitrogen (N) storage in agro-ecosystems represents an important strategy for ensuring food security and sustainable agricultural development in China. Accurate estimates of the distribution of soil C and N stores and their relationship to crop yield are crucial to developing appropriate cropland management policies. The current study examined the spatial variation of soil organic C (SOC), total soil N (TSN), and associated variables in the surface layer (0–40 cm) of soils from intensive agricultural systems in 19 counties within Henan Province, China, and compared these patterns with crop yield. Mean soil C and …

Nutrient Limitation In Three Lowland Tropical Forests In Southern China Receiving High Nitrogen Deposition: Insights From Fine Root Responses To Nutrient Additions, Feifei Zhu, Muneoki Yoh, Frank S. Gilliam, Xiankai Lu, Jiangming Mo

Frank S. Gilliam

Elevated nitrogen (N) deposition to tropical forests may accelerate ecosystem phosphorus (P) limitation. This study examined responses of fine root biomass, nutrient concentrations, and acid phosphatase activity (APA) of bulk soil to five years of N and P additions in one old-growth and two younger lowland tropical forests in southern China. The old-growth forest had higher N capital than the two younger forests from long-term N accumulation. From February 2007 to July 2012, four experimental treatments were established at the following levels: Control, N-addition (150 kg N ha–1 yr–1), P-addition (150 kg P ha–1 yr–1) and N+P-addition (150 kg N …

Nitrogen Fertilization Has A Stronger Effect On Soil Nitrogen-Fixing Bacterial Communities Than Elevated Atmospheric Co2, Sean Berthrong, Chris Yeager, Laverne Gallegos-Graves, Blaire Steven, Stephanie Eichorst, Robert Jackson, Cheryl Kuske

Sean Berthrong

Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO2 and N deposition. Using the nifH gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO2 conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO2 to affect these communities in the temperate pine forest. Based on data from Sanger sequencing …

Impacts Of Swine Manure Application And Alternative N-Management Practices On Productivity, Sustainability And Water Quality, Rameshwar S. Kanwar, Douglas Karlen, Cynthia A. Cambardella, Thomas Moorman, Thomas R. Steinheimer, Thomas S. Colvin

Douglas L Karlen

In the fourth year of this ongoing project, the effects of nine N-management practices under different tillage and cropping systems were evaluated. Forty experimental plots equipped with individual sumps and subsurface drainage metering and monitoring devices were used for the study. Overall results indicate that manure application rates and methods can be successfully managed for corn-soybean systems without damaging the water quality if the appropriate amount of N from swine manure can be applied.

Establishing A National Shellfish Sanitation Program In The Gambia, West Africa, Michael A. Rice, Foday Conteh, Karen Kent, Brian Crawford, Banja Bamba, Fatou Janha, Ismaila Bojang

Michael A Rice

A successful national program to assure sanitary quality of molluscan shellfish requires a multi-disciplinary and multi-agency governmental training, data collection, policy development and management effort in collaboration with members of the shellfish industry. The Tanbi Wetlands and other estuaries of Gambia support shellfisheries for oysters, Crassostrea tulipa, and the senile ark, Senelia senilis, conducted by the TRY Oyster Women’s Association. With low shellfish prices and a small local market, a Gambian National Shellfish Sanitation Program (GNSSP) was begun as a means to boost consumer confidence and allow market access to Gambia’s robust seasonal international tourism trade. Gambian officials began training …

Effects Of Temperature, Nutrients, Organic Matter And Coral Mucus On The Survival Of The Coral Pathogen, Serratia Marcescens, Erin Looney, Kathryn Sutherland, Erin Lipp

Kathryn Patterson Sutherland PhD

Serratia marcescens is an enteric bacterium that causes white pox disease in elkhorn coral, Acropora palmata; however, it remains unclear if the pathogenic strain has adapted to seawater or if it requires a host or reservoir for survival. To begin to address this fundamental issue, the persistence of strain PDL100 was compared among seawater and coral mucus microcosms. Median survival time across all conditions ranged from a low of 15 h in natural seawater [with a first-order decay constant (k) = −0.173] at 30°C to a maximum of 120 h in glucose-amended A. palmata mucus (k = −0.029) at 30°C. …

Human Sewage Identified As Likely Source Of White Pox Disease Of The Threatened Caribbean Elkhorn Coral, Kathryn Sutherland, James Porter, Jeffrey Turner, Brian Thomas, Erin Looney, Trevor Luna, Meredith Meyers, J. Futch, Erin Lipp

Kathryn Patterson Sutherland PhD

Caribbean elkhorn coral, Acropora palmata, has been decimated in recent years, resulting in the listing of this species as threatened under the United States Endangered Species Act. A major contributing factor in the decline of this iconic species is white pox disease. In 2002, we identified the faecal enterobacterium, Serratia marcescens, as an etiological agent for white pox. During outbreaks in 2003 a unique strain of S. marcescens was identified in both human sewage and white pox lesions. This strain (PDR60) was also identified from corallivorious snails (Coralliophila abbreviata), reef water, and two non-acroporid coral species, Siderastrea siderea and Solenastrea …

Human Pathogen Shown To Cause Disease In The Threatened Elkhorn Coral Acropora Palmata, Kathryn Patterson Sutherland, Sameera Shaban, Jessica L. Joyner, James W. Porter, Erin K. Lipp

Kathryn Patterson Sutherland PhD

Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments …

The Shellfish Corner -- Vibrios And Shellfish, Michael Rice

Michael A Rice

Pathogenic Vibrios are becoming an increasing problem for shellfish producers in North America and elsewhere. This paper reviews current research into the pathogenic nature of Vibrios and provides some practical advice for avoiding the propagation of Vibrios on shellfish farms nd in wild harvest molluscan shellfish.

The Molecular Dimension Of Microbial Species: 1. Ecological Distinctions Among, And Homogeneity Within, Putative Ecotypes Of Synechococcus Inhabiting The Cyanobacterial Mat Of Mushroomspring,Yellowstone National Park, Eric D. Becraft, Jason M. Wood, Douglas B. Rusch, Michael Kuhl, Sheila Jensen, Donald A. Bryant, David W. Roberts, Frederick M. Cohan, David M. Ward

Frederick M. Cohan

Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes (encoding a photosystem I reaction center protein subunit) and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper …

The Effect Of Dissolved Polyunsaturated Aldehydes On Microzooplankton Growth Rates In The Chesapeake Bay And Atlantic Coastal Waters, Peter J. Lavrentyev, Gayantonia Franzè, James J. Pierson, Diane K. Stoecker

Peter J. Lavrentyev

Microbial Isolations From Olive Ridley (Lepidochelys Olivacea) And Eastern Pacific Green (Chelonia Mydas Agassizii) Sea Turtle Nests In Guanacaste, Costa Rica, And Standard Testing Of Cloacal Fluid Antimicrobial Properties, Erin Keene, Tanya Soule, Frank Paladino

Tanya Soule

Microorganisms associated with olive ridley and East Pacific green turtle nesting and potential cloacal fluid antimicrobial properties were studied in Guanacaste, Costa Rica. During the 2010–2011 season, bacteria and fungi were isolated from olive ridley cloacal fluid, nest chamber sand, and egg samples. Because of the lack of cloacal fluid bacteria isolated, the focus of the 2011–2012 season shifted to determine whether fluid contained antibacterial properties by using Kirby–Bauer disk diffusion assays, and cloacal fluid and sand samples were taken to see whether bacteria were unique to cloacal fluid. Assays were performed on 34 olive ridley and 5 East Pacific …

National Park Service Cave Ecology Inventory And Monitoring Framework, Gretchen M. Baker, Steven J. Taylor, Shawn Thomas, Rick Olson, Kathy Lavoie, Marie Denn, Steven Thomas, Hazel Barton, Kurt Helf, Rene Ohms, Joel Despain, Jim Kennedy, David Larson

Hazel Barton

A team developed the Cave Ecology Inventory and Monitoring Framework for National Park Service (NPS) units. It contains information for NPS cave managers across the United States to determine how to inventory and monitor cave ecology. Due to the wide geographical scope of NPS caves and their many different types, the document does not prescribe exact protocols. Instead, it provides guidance for what types of inventory and monitoring are possible, a framework for deciding how to prioritize inventory and monitoring activities, and references to specific protocols that are already in place at NPS cave parks. Keywords: cave ecology, cave microbiology, …

Purification Of An Inducible Dnase From A Thermophilic Fungus, Kyle Landry, Andrea Vu, Robert Levin

Kyle S Landry