Ward, Dave M.

Dr. Dave M. Ward

Department of Land Resources and Environmental Sciences
Montana State University
Bozeman, MT
Project Summary: 

Species are fundamental units in plant and animal communities, but is this true in the microbial world? There is considerable debate as to whether bacteria evolve in fundamentally different ways than eukaryotes due to their rapid reproduction, rare (and promiscuous) sexuality, and evolutionarily significant gene exchange. Modern genetic and genomic analyses make  “named” bacterial species (traditionally demarcated by phenotypic properties) appear to be diverse, chaotic assemblages of rapidly exchanged genes. However, modern population genetics analysis challenges the concept that these named species are really biologically meaningful entities. Furthermore, natural patterning of genetic diversity and evolutionary theory suggest a more orderly concept of species as discrete ecologically adapted populations (ecotypes). Our conceptual framework is that ecotypes are the fundamental units of microbial communities that play a central role in linking genetic diversity to microbial community composition, structure and function. We will investigate a well-studied hot spring microbial mat community in Yellowstone National Park with ideal properties for employing sophisticated molecular methods. To understand how genetic diversity is organized in the mat community, we will compare (i) direct genomic sequencing of predominant mat populations (to objectively assay genomic diversity and determine how it is organized according to genetic criteria) with (ii) theory-driven population genetics analysis and evolutionary simulation designed to test for putative ecotypes. Genomic sequencing will enable development of microarray technology and high-throughput analysis of variant alleles that will be used to evaluate whether, as expected, putative ecotypes occupy unique niches and order gene distribution and expression within the mat community. The discovery of genetically separable ecotypes will broadly impact thinking in microbial evolution, systematics, ecology and physiology and will unify evolutionary principles across the breadth of size and complexity among organisms.

Broader Impacts:

Our team is a balance of young and established, male and female investigators from geographically and demographically diverse institutions.  The research integrates principles from general biology with microbiology and molecular biology, providing a cross-training opportunity that will help fill the chasm separating these fields.  Participants will share their disciplinary perspectives (microbial ecology, evolutionary biology, genomics and microbial physiology) with each other and the scientific community through a workshop series that will lead to web-based learning modules.  The microbial community is in Yellowstone Park, providing numerous opportunities for interaction with the park’s trained informal educators.  Preparation of new educational resources (e.g., resource manual for educating seasonal rangers and park managers, signage, trail guides, websites and exhibits for a new Visitor Education Center) will help millions of annual visitors, young and old, change the way they think about microorganisms. Five linked websites will broadly disseminate our databases and interpret the interdisciplinary importance of our work for nonscientists. Genomic websites will present sequences from direct mat analysis as well as two closely related, ecologically distinct pure-cultured thermophilic cyanobacteria (Synechococcus). Another website will describe the microarray in detail and report comparisons of gene expression in situ and in relevant Synechococcus isolates grown in laboratory culture.  A project website will collect all data, report tests of our main hypotheses, and serve as a conduit for dissemination of educational products.

  1. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments
    Frontiers in Microbiology, 2013
  2. Candidatus Thermochlorobacter aerophilum: an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics.
    International Society for Microbial Ecology Journal (ISME), 2012
  3. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.
    International Society for Microbial Ecology Journal (ISME), 2011
  4. Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat
    International Society for Microbial Ecology Journal (ISME), 2008
  5. Genomics, environmental genomics and the issue of microbial species
    Heredity, 2008
  6. Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
    Proceedings of the National Academy of Sciences, 2008
  7. Candidatus Chloracidobacterium thermophilum: An Aerobic Phototrophic Acidobacterium
    Science, 2007
  8. Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses
    International Society for Microbial Ecology Journal (ISME), 2007
  9. Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats
    Environmental Microbiology, 2007
  10. Archaeal and Bacterial Glycerol Dialkyl Glycerol Tetraether Lipids in Hot Springs of Yellowstone National Park
    Applied and Environmental Microbiology, 2007
  11. Impact of carbon metabolism on 13C signatures of cyanobacteria and green non-sulfur-like bacteria inhabiting a microbial mat from an alkaline siliceous hot spring in Yellowstone National Park (USA)
    Environmental Microbiology, 2007
  12. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats
    Proceedings of the National Academy of Sciences, 2006
  13. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function
    Philosophical Transactions of the Royal Society B, 2006
  14. Microbial diversity in natural environments: focusing on fundamental questions
    Antonie van Leeuwenhoek, 2006
  15. A Macrobiological Perspective on Microbial Species
    Microbe Magazine, 2006
  16. Diversity and Functional Analysis of Bacterial Communities Associated with Natural Hydrocarbon Seeps in Acidic Soils at Rainbow Springs, Yellowstone National Park
    Applied and Environmental Microbiology, 2005
  17. Diel Variations in Carbon Metabolism by Green Nonsulfur-Like Bacteria in Alkaline Siliceous Hot Spring Microbial Mats from Yellowstone National Park
    Applied and Environmental Microbiology, 2005
  18. Microbial Diversity in Hot Spring Cyanobacterial Mats:Pattern and Prediction
    Geothermal Biology and Geochemistry in YNP [TBI Text!], 2005
  19. The importance of physical isolation to microbial diversification
    FEMS Microbiology Ecology, 2004
  20. Compound-Specific Isotopic Fractionation Patterns Suggest Different Carbon Metabolisms among Chloroflexus-Like Bacteria in Hot-Spring Microbial Mats
    Applied and Environmental Microbiology, 2003
  21. Cyanobacterial Ecotypes in Different Optical Microenvironments of a 68°C Hot Spring Mat Community Revealed by 16S-23S rRNA Internal Transcribed Spacer Region Variation
    Applied and Environmental Microbiology, 2003
  22. Geographical isolation in hot spring cyanobacteria
    Environmental Microbiology, 2003
  23. Microscopic Examination of Distribution and Phenotypic Properties of Phylogenetically Diverse Chloroflexaceae-Related Bacteria in Hot Spring Microbial Mats
    Applied and Environmental Microbiology, 2003
  24. Alkane-1,2-diol-based glycosides and fatty glycosides and wax esters in Roseiflexus castenholzii and hot spring microbial mats
    Archives of Microbiology, 2002
  25. Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Molecular Analysis of Enrichments and Isolates Suggests Selection Based on Bioavailability
    Applied and Environmental Microbiology, 2000
  26. Highly Ordered Vertical Structure of Synechococcus Populations within the One-Millimeter-Thick Photic Zone of a Hot Spring Cyanobacterial Mat
    Applied and Environmental Microbiology, 2000
  27. Photoexcretion and Fate of Glycolate in a Hot Spring Cyanobacterial Mat
    Applied and Environmental Microbiology, 1988