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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.
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