David L. Erickson

Center for Devices and Radiological Health

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W. John Kress

National Museum of Natural History

Nathan G. Swenson

University of Notre Dame

María Uriarte

Columbia University

Jess K. Zimmerman

University of Puerto Rico System

Eric Wilson

Brigham Young University

Andrea Ottesen

United States Food and Drug Administration

Padmini Ramachandran

United States Food and Drug Administration

Jimena Forero‐Montaña

University of Puerto Rico at Río Piedras

Stuart J. Davies

ForestGEO

Jill Thompson

UK Centre for Ecology & Hydrology

Cooperative Institutions

National Museum of Natural History

Brigham Young University

Chinese Academy of Sciences

ForestGEO

Smithsonian Institution

Universiti Brunei Darussalam

Center for Food Safety and Applied Nutrition

United States Food and Drug Administration

Smithsonian Tropical Research Institute

University of Maryland, College Park

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PUBLIC INVOLVEMENT IN NATURAL RESOURCE PLANNING AND DECISION MAKING: A SELECTED BIBLIOGRAPHY.

David L. Erickson

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Mapping Biodiversity and Setting Conservation Priorities for SE Queensland’s Rainforests Using DNA Barcoding

PLoS ONE (2015)

Alison Shapcott Paul I. Forster Gordon P. Guymer William J. McDonald Daniel P. Faith

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

Tropical rain forest

Phylogenetic diversity

DNA Barcoding

10.1371/journal.pone.0122164

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Citations (54)

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys

bioRxiv (Cold Spring Harbor Laboratory) (2021)

J. Carl Craft Hyrum Edington Nicholas D. Christman John M. Chaston David L. Erickson

Abstract Turkeys ( Meleagris gallopavo ) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminant antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analysis of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella and E. coli when compared to domestic turkeys. E. coli strains isolated from wild or domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule ( kpsII , kpsIII ) or siderophore ( iroN , fyuA ) synthesis than those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. Importance Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compare the microbiota of wild and domestic turkeys. Results suggest that free ranging wild turkeys carry a distinct microbiome when compared to farm raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to farm raised birds. The microbiomes of wild turkeys may be used to guide development of new ways to control disease in large scale poultry production.

Poultry farming

Meleagris gallopavo

10.1101/2021.07.16.452759

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Water Department Practices and Regulations

American Water Works Association (1944)

Melvin P. Hatcher David L. Erickson John C. Detweiler W. Victor Weir

Weir

10.1002/j.1551-8833.1944.tb20015.x

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A MULTI-FRAME OF REFERENCE APPROACH TO LEISURE MOTIVATION

Social Behavior and Personality An International Journal (1975)

David Groves Harvey Kahalas David L. Erickson

With the increased amount of leisure time and ways to spend it caused by increased automation throughout the society, most individuals must facilitate utilization of their time to satisfy individual needs for proper maintenance of mental health. Therefore, the personality and social psychology of the individual within this setting must be examined critically. Research on this subject has been primarily of a descriptive nature, especially with regard to motivation. Therefore, this study was undertaken to lay a more quantitative framework for future research. A unique feature of this study was that it examined leisure from a multi-frame of reference, so that the changes in motivation and its important formative variables can be isolated with regard to content area and utilized to help individuals clarify their position to satisfy individual needs. The results indicate that emotion and involvement are the common elements that are related to leisure needs, and that the relationships among the interacting elements change as the frame of reference shifts.

Frame of reference

10.2224/sbp.1975.3.1.13

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The Stringent Response Is Essential for Pseudomonas aeruginosa Virulence in the Rat Lung Agar Bead and Drosophila melanogaster Feeding Models of Infection

Infection and Immunity (2011)

Stefanie Vogt Christopher Green Katarzyna M. Stevens Brad Day David L. Erickson

The stringent response is a regulatory system that allows bacteria to sense and adapt to nutrient-poor environments. The central mediator of the stringent response is the molecule guanosine 3',5'-bispyrophosphate (ppGpp), which is synthesized by the enzymes RelA and SpoT and which is also degraded by SpoT. Our laboratory previously demonstrated that a relA mutant of Pseudomonas aeruginosa, the principal cause of lung infections in cystic fibrosis patients, was attenuated in virulence in a Drosophila melanogaster feeding model of infection. In this study, we examined the role of spoT in P. aeruginosa virulence. We generated an insertion mutation in spoT within the previously constructed relA mutant, thereby producing a ppGpp-devoid strain. The relA spoT double mutant was unable to establish a chronic infection in D. melanogaster and was also avirulent in the rat lung agar bead model of infection, a model in which the relA mutant is fully virulent. Synthesis of the virulence determinants pyocyanin, elastase, protease, and siderophores was impaired in the relA spoT double mutant. This mutant was also defective in swarming and twitching, but not in swimming motility. The relA spoT mutant and, to a lesser extent, the relA mutant were less able to withstand stresses such as heat shock and oxidative stress than the wild-type strain PAO1, which may partially account for the inability of the relA spoT mutant to successfully colonize the rat lung. Our results indicate that the stringent response, and SpoT in particular, is a crucial regulator of virulence processes in P. aeruginosa.

Pyocyanin

10.1128/iai.00193-11

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A link between zinc uptake, bile salts, and a capsule required for virulence of a mastitis-associated extraintestinal pathogenicEscherichia colistrain

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Mark A. Olson Aleksander Grimsrud Amanda C. Richards Matthew A. Mulvey Eric Wilson

ABSTRACT Extraintestinal pathogenic Escherichia coli (ExPEC) are major causes of urinary and bloodstream infections. ExPEC reservoirs are not completely understood. Some mastitis-associated E. coli (MAEC) strains carry genes associated with ExPEC virulence, including metal scavenging, immune avoidance, and host attachment functions. In this study, we investigated the role of the high-affinity zinc uptake ( znuABC ) system in the MAEC strain M12. Elimination of znuABC moderately decreased fitness during mouse mammary gland infections. The Δ znuABC mutant strain exhibited an unexpected growth delay in the presence of bile salts, which was alleviated by the addition of excess zinc. We isolated Δ znuABC mutant suppressor mutants with improved growth of in bile salts, several of which no longer produced the K96 capsule made by strain M12. Addition of bile salts also reduced capsule production by strain M12 and ExPEC strain CP9, suggesting that capsule synthesis may be detrimental when bile salts are present. To better understand the role of the capsule, we compared the virulence of mastitis strain M12 with its unencapsulated Δ kpsCS mutant in two models of ExPEC disease. The wild type strain successfully colonized mouse bladders and kidneys and was highly virulent in intraperitoneal infections. Conversely, the Δ kpsCS mutant was unable to colonize kidneys and was unable to cause sepsis. These results demonstrate that some MAEC may be capable of causing human ExPEC illness. Virulence of strain M12 in these infections is dependent on its capsule. However, capsule may interfere with zinc homeostasis in the presence of bile salts while in the digestive tract.

Strain (injury)

Capsule

10.1101/2020.06.25.172775

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Supplement 1. All python/STAN code, including Bayesian hierarchical model, used in the analysis.

Figshare (2016)

Nathan P. Lemoine Jessica Shue Brittany Verrico David L. Erickson W. John Kress

File List Supplement_Model_REPORT.txt (MD5: ea2e3f2c6f17b80e7d3b55eff718d9d3) Description Supplement_Model_REPORT.txt contains all Python/STAN code needed to replicate the analysis and hierarchical model.

Python

10.6084/m9.figshare.3563106

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Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot

PLoS ONE (2010)

W. John Kress David L. Erickson Nathan G. Swenson Jill Thompson María Uriarte

Background Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny. Methodology/Principal Findings Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history. Conclusions/Significance As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Phylogenetic diversity

Supermatrix

DNA Barcoding

10.1371/journal.pone.0015409

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Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes

PLoS ONE (2013)

Carlos García‐Robledo David L. Erickson C. L. Staines Terry Erwin W. John Kress

Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (rbcL, trnH-psbA and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (rbcL and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The rbcL locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt's sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.

DNA Barcoding

Guild

10.1371/journal.pone.0052967

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Citations (171)