| home | lab members | c.v. | publications | courses |

 

 

Scott Kelley
Assistant Professor
Department of Biology
San Diego State University

5500 Campanile Drive
San Diego , CA 92182-4614 USA

Email: skelley@sciences.sdsu.edu
619 594 5371 (phone)
619 594 5676 (fax)

Degree Programs:
Cell and Molecular Biology, M.S.
Doctoral Program with UCSD, Ph.D.
Evolutionary Biology, M.S.
Computational Sciences Program M.S.

Affiliations:
Center for Applied and Experimental Genomics
Center for Microbial Sciences

 

NEW IN THE LAB

See our most recent papers in Nature, Environmental Microbiology, Molecular Phylogenetics and Evolution and soon in Nucleic Acids Research.

 

 

 

 

 

 

Main Projects

My lab combines phylogenetic (Bioinformatics) methods and culture-independent molecular tools to study environmental microbiology. The discipline of molecular phylogenetics uses information from DNA or proteins to reconstruct the evolutionary history of life. One of the most powerful applications of molecular phylogenetics has been in the field of environmental microbiology. Less than 1% of the existing microbial diversity on the planet has been cultured, and a growing number of molecular studies have revealed that standard culturing methods significantly underestimate the microbial diversity of environmental communities. The development of culture-independent techniques based on the amplification of small-subunit ribosomal DNA (16S rRNA gene sequences) from biological samples has revolutionized our understanding of microbial diversity. Scientists have uncovered astounding microbial diversity in everything from hot springs to soils to shower curtains. Combined with computational phylogenetic approaches, culture-independent molecular approaches allow us to discover thousands of new organisms, infer biological properties of these uncultured organisms, and determine their role in the environment. In our lab, we apply molecular phylogenetics and culture-independent approaches in three main areas:

Microbial diversity in extreme environments
Our lab has an on-going collaboration with Dr. Rick Bizzoco (SDSU) and Dr. Rob Knight ( University of Colorado , Boulder ) to study the phylogenetic diversity of microbial communities living in acidic thermal springs and steam fumaroles around the world. Using phylogenetic methods and carefully controlled studies, we have explored the relationship between sediment chemistry and bacterial diversity. More recently, we have developed sampling methods to collect and examine microbial diversity of geothermal spring waters as they are pumped out of the ground. This has allowed us to determine the contribution of the subsurface to surface sediment communities, assess the degree of geographic isolation of geothermal communities, and discover bacterial divisions with no cultured representatives. We are also the first group to develop efficient sterile sampling methods for high temperature (120 C) steam vents (fumaroles). Our study environments so far have included Yellowstone National Park, Lassen National Park, New Mexico, Hawaii, Kamchatka (Russia), and Italy.

Culture-independent analysis of bacterial contamination in human environments.
Human environments provide fascinating and complex habitats for microbial diversity. However, despite the fact that Westerners spend approximately 90% of their time indoors, we know extremely little about the diversity of microbes in these environments. Our studies of daycare centers, therapeutic pools, shower curtains and airplanes have shown human environments to contain a rich mixture of environmental (soil, water) and human-associated microbes. Moreover, each of the artificial environments appears to select and enrich for particular groups of microbes depending on physical and chemical conditions. For example, warm hospital pools enrich for Mycobacteria, shower curtains contain Sphingomonads and Methylobacteria, and daycare surfaces are covered with slime-producing Pseudomonads. The degree of contamination from human sources (oral, skin, fecal…etc.) underscores the potential for rapid pathogen spread in these environments.

Emerging infectious diseases in wild animal populations.
In collaboration with researchers at the University of Idaho , we have been using culture-independent approaches and phylogenetic methods to determine the bacterial diversity of the respiratory tract of healthy bighorn sheep. North American bighorn sheep provide a model system for the study of animal-associated microbiota in small natural populations. In the twentieth century, most of the southern populations of these animals have gone extinct, including all native populations in Washington , Oregon , and neighboring regions of southwestern Idaho and northeastern California . Respiratory diseases have been a major, perhaps the major, contributor to problem and have foiled many recent efforts at reintroduction. The primary culprit appears to be the spread of disease from domesticated sheep, but identifying responsible pathogens has been difficult using the standard culturing methods. Our studies have shown that bighorn respiratory tracts harbor many bacteria missed by culturing methods and we have also found evidence of potential new disease organisms (Histophilus somni, Psychrobacter sp., and Moraxella sp.) in the lungs of dead sheep. We have also complete phylogenetic studies of Pasteurella trehalosi and Mannheimia haemolytica strains, and studies of horizontal gene transfer of the leukotoxin operon among strains and bacterial species in wild bighorn populations. We are currently developing rapid culture independent methods to identify the cause and source of illnesses.

Other Projects

Students are exploring several other areas of research in my lab, including Bioinformatics methods development (software) and studies involving bark beetles (Coleoptera: Scolytinae), one of the most diverse, destructive and biologically interesting insect groups in the world. The bark beetle related projects include: (1) A population genetics study of the sib-mating palm-seed borer beetle in California ; (2) Phylogenetics of the bark beetle genus Dendroctonus based on multiple nuclear loci; and (3) Studies of bacteria symbionts associated with bark beetles. We have also collaborated with researchers at SDSU and at other institutions on phylogenetic and molecular evolution projects on topics as diverse as marine phage community structure, coral reef ecology, amphibian and reptile phylogenetics, and mouse virus evolution. Given my boundless interest in the natural world, we are never bored in the Kelley Lab!

Bioinformatic Method Development
I have students developing algorithms on a variety of topics, including: (1) Isolation by Distance – Software that detects patterns of genetic isolation by distance among natural populations; (2) Gene Regulatory Module Motif Searching – Detecting clusters of sequences motifs in co-regulated genes; and (3) Methods that use phylogenetic trees to improve gene function identification.