The Garey Lab Page Selected Publications Members of the Lab
Welcome to the website for the research
laboratory of Dr. Jim Garey in the Department of Cell Biology,
Microbiology and Molecular Biology at the University of South
Florida. My laboratory focuses on using molecular and
morphological tools to study biodiversity in underwater coastal
caves, vents and sinkholes as well as inland soils worldwide.
Earlier work in my lab focused on molecular phylogeny of the
animal kingdom.
Coastal Underwater Cave and Karst
Biodiversity (Note: If you are a cave certified diver with a B.S. in
Biology and interested in graduate school, please contact Dr.
Garey)
We have been studying the biodiversity and environments of cave
and karst systems in Florida for the past decade. We are carrying
out a long term study of an offshore sinkhole in the Gulf of
Mexico known as Jewfish Sink.This sinkhole is 1 km offshore and
appears as an 5 meter opening in the shallow rocky bottom of the
Gulf of Mexico. The opening is approximately 2 meters below
the surface of the Gulf, and continues to a depth of 65 meters and
the sink widens to about 30 meters. At one time it had a direct
connection to the Floridan aquifer and was an active submarine
freshwater spring. In 1962, during a drought and after an
extensive citrus industry was established onshore, the spring
ceased flowing and became an anaerobic marine basin that becomes
stratified and has limited connectivity with the Gulf above. This
work was carried out primarily by a former graduate student, Michael
Garman. We have studied the biogeochemical changes
that occur seasonally (Garmen et al., 2005) and surveyed the
biodiversity in and around the sink using our Molecular Profiling
method as well as more conventional morphological evaluations
(Garman et al. 2011). Haydn Rubelmann, a PhD student in my
lab is continuing this work, focusing on changes to the bacterial
community that drive the seasonal changes in
biogeochemistry. Several years ago, another PhD student,
Damian Menning and I began to study an active coastal spring named
Double Keyhole Spring, located in a salt marsh near Jewfish Sink.
This is a brackish spring that is still flowing, but at high tide,
the flow often reverses, bringing Gulf water into the Floridan
Aquifer, demonstrating the consequences of aquifer overuse that
leads to salt water intrusion and could be a mechanism for Gulf
oil spills to contaminate the onshore aquifer. We are studying the
hydrogeology and biogeochemistry of the system, as well as the
biodiversity of bacteria and microbial eukaryotes in the water
column and the sediment within the cave. All of this work
has involved extensive cave diving. You can get an idea of what
this is like by viewing this >>>> video
<<<< of the Double Keyhole project.
Dr. Jim Garey with
graduate student Damian Menning at Double Keyhole cave in
Florida.
Studies of an arsenic-rich active shallow-water submarine vent
in Papua New Guinea
Tutum Bay is a remote site on Ambitle Island in Papua New
Guinea where several arsenic rich shallow water hydrothermal vents
are located. Former graduate student Dave Karln and I were members
of a team from USF that was awarded an NSF Biocomplexity grant to
investigate the geochemistry and biocomplexity of this site. We
made two extensive field trips to the site, which consists of
several hydrothermal vents at a depth of about 8 meters that are
situated within a coral reef system. The hot vent fluid is derived
from rain water on the island that percolates to an
aquifer containing arsenic deposits and heated by extensive
volcanic activity. The analyses are still ongoing, but an overview
has been published (Pichler et al 2006) as has a
macrofauna analysis from the first field season (Karlen et al.
2010). We used molecular profiling to look at sediment bacteria,
microbial eukaryotes and meiofauna and conventional morphological
methods for meiofauna and macrofauna. We are currently
investigating the ecological interactions between the
geochemistry, bacteria and meiofauna present at the site. Thus
far, our studies have revealed that the effect of the vents
extends much further than expected, and that there are distinctive
changes in biological communities along a transect extending 300
meters from the vent we studied.
Left: Tutum Bay and
Ambitle Island in Papua New Guinea, Right: Dave Karlen and Roy
Price collect pore water samples in Tutum Bay.
Soil Global Biodiversity
(see more about this project here)
We are studying the diversity of small soil animals (mesofauna)
in order to find out (1) if there is a relationship between below
ground biodiversity and above-ground biodiversity and (2) whether
or not small soil animals are more likely than above ground
organisms to be cosmopolitan in distribution. This project was
funded by an NSF grant and is a collaborative effort involving
Diana Wall at Colorado State University and Richard Bardgett at
University of Lancaster in the UK . My lab developed a method of
"molecular profiling" which allowed us to investigate a cross
section soil animals in a sample by extracting DNA directly from
soil samples and then analysing the DNA sequences of the 18S rRNA
gene. This work has involved many people in my lab, but was mostly
done by a postdoctoral fellow, Tiehang Wu, who is now an assistant
professor at Georgia Southern University. Using phylogenetic
methods, we found we could estimate the number and taxonomy of
species from the DNA sequence information. This data is
subsequently analysed using statistical software developed for
community structure in the context of environmental
parameters. The methods are described in a paper from my lab
(Wu et al. 2009) that presents an analysis of small soil animals
at two sites in Alaska, one tundra and one aboreal forest. The
project ultimately involves 11 sites globally that encompass many
kinds of biomes such as tropical and temperate forests,
grasslands, tundra and boreal forests. The bigger study is was
published in PNAS in October of 2011 and the findings suggest that
below-ground biodiversity may be inversely related to above-ground
biodiversity, and that true cosmopolitan species are extremely
rare.
Above left. Drs. Ed Ayres and
Johnson Nkem measuring soil respiration in Costa Rica.
Above right: Dr. Jim Garey in Costa Rica.
Above left: Jim Garey loading a sample into the DNA
sequencer. Above right: Buffalo at the Konza Prairie
soil field site.
Phylogenetic Studies
My laboratory has played a major role in broad level animal
phylogenetics and was resoponsible in part for the discovery of
Ecdysozoa, a large clade of moliting protostome animals (Aguinaldo
et al.1997). We also participated in a major revision of nematode
phylogeny (Blaxter et al. 1998), and discovered that the Phylum
Acanthocephala, a group of large parasitic worms are simply giant
parasitic rotifers (Garey et al. 1996) and have been involved in
Tardigrade phylogeny and taxonomy. More recently, Alan Franck, a
graduate student in my lab has been studying the biogeography and
phylogeny of Harrisia,
a cactus group found in South America, the Caribbean and Florida.
His work suggests that Harrisia
is a monophyletic genus and is divided into two subgenera, four
sections, and two subsections. This study shows that Harrisia may
have originated in the Andes and later dispersed into Brazil
before further speciation in the Gran Chaco or the Caribbean.
Genomics
My laboratory is involved in comparative genomics and carried
out a comparative study of several invertebrate genomes (Mushegian
et al. 1999) that demonstrated that different animals evolve at
different rates. We also have carried out research in the area of
codon reassignment (Massey & Garey 2007). Currently, Roy
Vaughn, a graduate student in my lab is describing the
transcriptome of a brittle star species and comparing it to the
transcriptome of the sea urchin. This study is in the
context of signalling pathways important in embryo development and
is in collaboration with Dr. Brian Livingston at California State
University, Long Beach.