Title: Myakka
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Title: Myakka
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Creator: Department of Soil and Water Science. Institute of Food and Agricultural Sciences. University of Florida.
Publisher: Department of Soil and Water Science. Institute of Food and Agricultural Sciences. University of Florida.
Publication Date: Fall 2008
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contents
Research Activities in Soil
Microbial Ecology Laboratory
Microbial Community in Wetlands
Entomopathogenic Nematode
Spatial Patterns
Who Listens when Microbes Talk?
Biofilm Communities
Microbial Conversion for
Bioenergy & Waste Treatment
Faculty, Staff, & Student News
William Reve
From Our Former Students


EDITORS:
Susan Curry
scurry@ufl.edu

Dr. Vimala Nair
vdn@ufl.edu



UNIVERSITY f
UFLORIDA
PFAS


http://soils.ifas.ufl.edu


Microbial Ecology Programs

From the Chair...


Microbial ecology is changing at an
exceptionally rapid rate, particularly with
the development of new methods and
increased understanding of the
importance of microorganisms to
fundamental processes in soils and
waters. Naturally occurring
microorganisms are involved in virtually
all processes in soil and water, ranging
from pedogenesis and elemental cycling,
to the detoxification of environmental
pollutants. Human activities can impact
many of these processes, and a clear
understanding of the fundamental
controls on microbial activities is required
to predict the directions and magnitudes
of these activities.

The Soil and Water Science Department
(SWSD) has been very active in research
and education on the role of
microorganisms in regulating water
quality including pathogens, remediation
of contaminated sites, ecosystem
restoration, sequestration of carbon,
production of greenhouse gases, and plant
productivity. These little giants play a
major role in regulating various functions
in the ecosystems (agriculture lands,
forested lands, range lands, urban lands,
and wetlands and aquatic systems) we
study in our department. The microbial
ecology programs of Ogram, Graham, and
Teplitski are well integrated into all
research thrust areas of the department.

Future directions in soil and water
microbial ecology are difficult to predict


given the speed at which the science is
changing; however, the general trend is
toward linking microbial activities across
scales, and it is in this general area that a
significant thrust of SWSD's future efforts
are directed. Many, if not most,
environmental processes that are
observed at landscape and watershed
scales are affected at the microscale:
interactions among and between
microorganisms and their immediate
environment are responsible for many
processes that regulate ecosystem
functions. Detailed characterization of
these processes at the scale of the
bacterial cell and smaller, to the
interface between the cell and its
substrate (e.g. mineral, plant receptor, or
environmental contaminant) is required to
fully understand processes at higher
scales. Soil and water microbiology is, by
nature, interdisciplinary, and research
across such broad scales will require
collaboration between a variety of
disciplines, including microbiologists,
mineralogists, physicists, chemists, and
scientists with the ability to synthesize
and model these interactions across
scales. The department is committed to
strengthening soil and water microbiology
programs to address current and future
needs of our clientele, while advancing
the science in this area. In this
newsletter we highlight select programs
related to microbial ecology in soil,
water, and environmental sciences.

VAfLpW- -








Research Activities in Soil Microbial Ecology Laboratory

The Soil Microbial Ecology Laboratory (http://molecol.ifas.ufl.edu) led by Andy
Ogram is engaged in a range of activities that include research, teaching, and a
service component. We recently received funding to continue investigating
linkages between microbial community structure and function in nutrient
impacted regions of the Everglades, and, with collaborators in the UF College of
Medicine, will use a highly innovative approach using functional microarrays to
evaluate controls on methanogenesis and sulfate reduction.

An on-going project includes identification and optimization of microbial
processes leading to degradation of the banned, but persistent, pesticide DDT
Sand its daughter products DDE and DDT in organic soil from around Lake Apopka.
Graduate student Hiral Gohil is currently enriching bacteria that are capable of
utilizing DDT as a terminal electron acceptor, a process that appears to result in greatest loss of DDT and DDE in her
studies. DDT is also highly hydrophobic, a property that greatly decreases its availability for microbial attack in organic
soils. Hiral will soon begin investigating novel approaches to increasing the bioavailability of DDT for microbial attack.

Haryun Kim has been working with us to investigate nitrogen dynamics in an area of the Santa Fe watershed that is
impacted by cattle and nursery operations. Haryun is using a combination of biochemical and molecular ecological
approaches to define controls on different routes for nitrogen cycling at the site.

Abid Al-Agely runs the Soil Microbiology Core facility, and is active in research, teaching, and service activities. He
conducts a practical short-course on his area of specialization, mycorrhizal fungi, every summer
(http://conference.ifas.ufl.edu/soils/micro/index.html). In addition, he manages the service arm of the core facility, for
which he conducts a range of biological assays for customers. These assays include mycorrhizal inoculum potential and
mycorrhizal colonization assays, as well as production of inocula. For additional information on soil microbial ecology
programs, contact Andy Ogram at aogram@ufl.edu.


Microbial Community in

Wetlands

Phospholipid fatty acid analysis (PLFA) is based on the determination of
"signature" lipid biomarkers from the cell membranes and walls of
microorganisms. Phospholipids are an essential part of intact cell
membranes, and information from the lipid analysis provides
quantitative insight into three important attributes of microbial
communities: viable biomass, community structure, and nutritional
status. We in the Wetland Biogeochemistry Laboratory are currently
using PLFA profiles to characterize microbial community composition in
several wetland ecosystems. This technique was applied in the
restored wetlands of the Hole-in-the-Donut (HID) region of the Everglades
National Park, Florida. We found that 1) there was accretion of organic
matter and general shift from N limitation in restored younger sites to P
limitation in the older sites, 2) soil microbial community in restored sites
were different from that in the native vegetation site, 3) seasonal variation
(dry versus wet) in microbial community composition in younger restored
sites was greater than relatively older sites. Communities in restored sites
were characterized by higher relative abundance of fungal biomarkers and
higher ratios of gram negative to gram positive compared to the
undisturbed native vegetation site. The biomarker for actinomycetes was found to be significantly correlated with
phosphorus concentrations in soils. There did not appear to be any association between fungal biomarkers and soil P.
Our results indicate that extreme restoration processes may influence the ecosystem development processes by
influencing the microbial community composition for a short term.
For additional information, contact Kanika Sharma at: kanika@uft.edu








































Welcome... Incoming Students
Summer and Fall 2008


Subodh Acharya, PhD (Rao Mylavarapu)
Elena Azuaje, MS (Nick Comerford)
Pamela Brown, MS (Alan Wright)
Maninder Chahal, MS (Gurpal Toor)
Hao Chen, PhD (Lena Ma)
Aldo Fritz, PhD (Amy Shober)
Sean Fromang, MS (Chris Wilson)
Lisa Gardner, PhD (Ramesh Reddy)
Ashok Garg, PhD (Rao Mylavarapu)
Piyasa Ghosh, PhD (Lena Ma)
Luke Gommerman, MS (Rex Ellis)
Hollie Hall, PhD (Jim Jawitz)
Amy Hylkema, MS (Amy Shober)
Matthew Jablonski, MS (Gurpal Toor)


Michael Jerauld, MS (Jim Jawitz)
Dakshina Kadiyala, PhD (Yuncong Li/Rao Mylavarapu)
Davie Kadyampakeni, PhD (Kelly Morgan/Peter Nkedi-Kizza)
Kamaljit Kamaljit, PhD (Gurpal Toor)
Jongsung Kim, PhD (Sabine Grunwald)
Jason Lessl, PhD (Lena Ma)
Cassandra Medvedeff, PhD (Patrick Inglett)
Lucy Ngatia, PhD (Ramesh Reddy/ Ben Turner)
Travis Roberts, MS (Carl Fitz)
John Rowland, PhD (John Cisar)
Kiara Winans, PhD (Ramesh Reddy)
Dana Woolley, MS (Patrick Inglett)
Richard Yudin, PhD (Yuncong Li)
Tan Xu, MS (Alan Wright)


Do Natural Enemies Regulate Entomopathogenic

Nematode Spatial Patterns?

Entomopathogenic nematodes (EPN) have been shown to be important
natural enemies of Diaprepes abbreviatus, a major weevil pest of citrus
in Florida and the Caribbean Basin. In regions where endemic EPN
species diversity and predation of weevil larvae are high, the insect is a
minor pest; whereas, the weevil can cause growers to abandon
citriculture in regions with fewer species and little predation by EPN.
Accordingly, we are studying biotic and abiotic factors that regulate
spatial patterns of EPN across the Florida citrus industry.
Nematophagous fungi (NF) have been shown to respond in a density
dependent manner to EPN when they emerge in high numbers from
insect cadavers and when EPN are added to soil as an augmentation biocontrol tactic. Predation rates by NF also
vary depending on the species combinations of NF and EPN, suggesting the possibility that some EPN species may
have a competitive advantage in habitats that favor particular NF. Among the EPN endemic in Florida citrus
groves, the numbers of Steinernema diaprepesi and S. glaseri were unaffected by three species of Arthrobotrys
(trapping fungi) in soil bioassays, whereas numbers of Heterorhabditis indica, H. zealandica and S. riobrave were
reduced significantly. In contrast, two endoparasitic fungi (Catenaria sp. and Myzocytium sp.) whose zoospores
require free water to locate and infect nematodes, had no effect on numbers of H. indica, but preyed heavily on
the other four EPN species. H. indica is frequently the dominant species detected in parts of Florida with poorly
drained soils and high water tables. Ongoing research is characterizing the spatial patterns of NF in Florida to
better understand their habitat requirements and their potential to affect EPN communities. For additional
information, contact Jim Graham at: ihgrahm@ufl.edu.









Who Listens when Microbes Talk?


What started as a project on understanding the intricacies of bacterial
cell-to-cell communications in a symbiosis between a model Legume
Medicago truncatula and its bacterial partner, Sinorhizobium meliloti,
has led to some exciting new discoveries that could potentially lead to
developing biological control for coral diseases and improving safety of
-minimally processed foods, like oysters and vegetables.

In the Microbial Community Ecology Laboratory, Mengsheng Gao has
identified two novel bacterial genes that may function in detecting
bacterial quorum sensing signals. She has also discovered what looks
like a regulatory RNA, a molecular "switch" that may help further time
the onset of "quorum." Bacteria rely on quorum sensing to detect
whether the number of individuals within a population reached a
certain threshold at which enough bacteria are present for a coordinated attack on a plant or animal host. By learning
to manipulate bacterial quorum sensing, it may very well be possible to develop novel pharmaceuticals that do not kill
the pathogen, but rather specifically interfere with the ability of a pathogen to cause a disease. It should also be
possible to "trick" the bacteria into aggregating into multicellular clumps, so that these clumps could then be removed
by catching them in microscopic traps.

Studies of cell-to-cell communication in host-associated microbial communities have led
to several exciting collaborations. Clayton Cox (above), who joined the Teplitski group
recently, was awarded a prestigious NSF Graduate Student Fellowship to learn about the
role of cell-to-cell signaling in the interactions between native oyster-associated
microbes and the invading human pathogens. In collaboration with Dr. A.C. Wright
(Department of Food Science and Human Nutrition), Clay also plans to find how to use
this knowledge to improve microbiological safety of raw shellfish.

Cory Krediet and Stephanie Halbig in collaboration with Dr. Kim Ritchie (Mote Marine
Laboratory) are learning whether it will be possible to develop biological control
formulations for treating coral diseases. Cory (right) is an Alumni Fellow and a Ph.D.
candidate in Interdisciplinary Ecology; his NSF Fellowship application was awarded an Honorary Mention.

For additional information, contact Max Teplitski at: maxtep@ufl.edu



Soil and Water Science Distinguished Seminar
Dr. Don Sparks, S. Hallock du Pont Chair of Soil Chemistry and Department Chairman
University of Delaware, presented the key note lecture on "Shining Light on Biogeochemical
Processes in the Earth's Critical Zone at the 9th Annual SWS Research Forum, September 12, 2008.

Dr. Sparks is internationally recognized for his research contributions in the areas of: kinetics of
soils chemical processes, surface chemistry of soils and soil components using in-situ spectroscopic
and microscopic techniques. Dr. Sparks Environmental Soil Chemistry Laboratory focuses on how
toxic metals such as arsenic, nickel, and zinc and plant nutrients such as phosphorus and sulfur are bound (sorbed) on
soils. His research uses bright light sources generated at syncrotron facilities (associated with National Laboratories)
to determine the forms (species) of the metals and nutrients in the soil at the molecular scale. This information is
necessary to make accurate predictions about how easily the contaminant will leach into the water supplies, and
determine its toxicity and bioavailability to plants, animals, and humans. His research also conducts speciation
research on metal contaminated soils and on plants that accumulate large quantities of metals (hyper-accumulators).
The results of these studies are useful in developing effective strategies for soil remediation. Additional details of his
research and teaching programs can be found at: http://ag.udel.edu/plsc/faculty/sparks.htm










Biofilm Communities:

The Everglades Periphyton

Within open water slough environments of the Florida Everglades, periphyton represents the main source of
primary production. These "biofilm communities" are complex structures composed primarily of cyanobacteria
and algae, but also contain significant bacterial biomass. Current research is identifying and quantifying
molecules and macromolecules that will influence the myriad of roles of the biofilms from their potential
palatability at the base of the food web to their functionality within the wetland environment. This project is
conducted in collaboration with the South Florida Water Management District (Scot Hagerthey and Sue
Newman).

In the high mineral, low P areas of the Everglades, cyanobacterial
dominated periphyton mats dominate. The mats from WCA-2a have been
found to contain four different cyanotoxins, ranging from neurotoxins to
skin irritants, potentially further deterring would be grazers. In addition
to having a high C:P ratio and toxins present, these mats also precipitate
large amounts of calcium carbonate, resulting in encrustation of the mats.
Deposition of calcite is on the extracellular sheaths and polymers (EPS)
secreted by the cyanobacteria. Biochemical analyses of the
polysaccharides that make up these polymers indicate a glucose, xylose,
and fucose rich polymer. Conversely, in low mineral, low P areas of the
Everglades (WCA-1), desmid dominated periphyton mats dominate and do
not precipitate calcium carbonate. The EPS secreted is reflective of the
desmids, and polymers contain significant proportions of glucose, Epipelon collected from the interior
galactose, and mannose, in addition to arabinose, xylose and fucose. of WCA-2a. Diatoms and some
Increased mineral content of the filamentous algae evident, majority
water along with the biochemical of the cyanobacteria and EPS
structure of the EPS within the material is calcified.
biofilms from WCA-2a results in an
overall increase in cohesive strength, making these mats capable of
stabilizing sediments, an important role regulating sediment transport.

This research helps to understand ecosystem function of the abundant
periphyton mats within the Florida Everglades. This research will not only
be used in the broader context of comparison of functionality with other
wetland ecosystems, but also when making management decisions to
determine how habitat manipulations will affect the base of the food web.
For additional information contact Brent Bellinger at: bbelling@sfwmd.gov
Periphyton collected from the interior
of WCA-1. Diatoms and desmids
visible within EPS matrix.










Microbial Conversion for Bioenergy

and Waste Treatment

The Bioenergy and Sustainable Technology Laboratory conducts basic and applied research on environmental
biotechnology, with particular emphasis on anaerobic microbiology and the practical application of anaerobic
digestion technology for waste management/treatment and renewable energy production from biomass and
organic residues. Our optimization of robust biodigester ecosystems is rooted in the modular arrangement of
metabolic functions that microbial guilds perform in nature.

Anaerobic digestion is a process by which a
complex mixture of symbiotic
microorganisms transforms organic materials
under oxygen-free conditions into biogas, a Hydrolys
mixture of mostly methane and carbon m lonomeo Oigiumm
dioxide. Anaerobic digestion occurs ^wAcdogene
naturally in anaerobic environments, such as Organic Acids
landfills, sediments, saturated soils and Acetogenesi
animal intestinal tracts. In practice, Acetate -- H- C
anaerobic digestion is the engineered Methanogenesls
methanogenic decomposition of organic
matter carried out in reactor vessels, called
digesters. As much as 90% of the
biodegradable organic fraction of a waste My of A c
Microbiology of Anaerobic Digestion
can be stabilized in anaerobic treatment by
conversion to methane gas. Since the
process uses a mixed microbial culture, no sterilization step is required and the diversity of microbial species
confers fermentation stability and substrate independence. Under controlled conditions, anaerobic digestion
offers a holistic treatment solution that stabilizes wastes, controls odors, reduces pathogens, minimizes
environmental impact from waste emissions, and maximizes resource recovery while simultaneously being a net
energy producer. The co-products of anaerobic digestion nutrients and fiber reduce the need for synthetic
fertilizers and soil conditioners that are produced using less sustainable methods, providing cost savings and
environmental benefits. Nutrients contained in the organic matter are conserved and mineralized to more
soluble and biologically available forms, providing a more predictable biofertilizer.

For further information, visit Biogas A Renewable Biofuel or contact Ann Wilkie at acwilkie@ufl.edu.



Southern Rlegional Cooperative Soil
Survey Conference
^^ J Innova-tive Technologies for the New Soil Survey
July 14-17, 2008, Gainesville, FL
(http://conference.ifas.ufl.edu/SSC/)

This conference was hosted by UF-SWSD (chair: S. Grunwald) and Natural
Resources Conservation Service (NRCS) (co-chair: D. Peterson) aiming to bring
together representatives of the National Cooperative Soil Survey in the southern
states for discussion of technical, scientific, and general questions and issues. Topics ranged from digital methods and
technologies such as GIS, geospatial analysis, remote sensing LIDAR, soil spectroscopy, soil sampling designs, web
applications and database management. A status report of the current national soil survey program was presented by
Micheal Golden, Director Soil Survey, NRCS Washington D.C. A field trip that focused on Florida soils and a
demonstration of digital soil mapping techniques complemented the conference.








Faculty, Staff, and Students
Ann Wilkie has been named winner of the third annual Florida Energy Achievement
Award. The award, presented by the Florida Solar Energy Center (FSEC), recognizes a
company, organization, or individual that has made a significant achievement in the
efficient utilization of energy, energy conservation, energy education, or renewable
energy in the state of Florida.

Nick Comerford was elected as the 2009 President of Soil Science Society of America.
Nick has accepted the Center Director's position at the North Florida Research and
Education Center, Quincy, Florida.

Yuncong Li was awarded the Wachovia Extension Professional Award for his outstanding
contributions in extension and outreach.

Tom Obreza was awarded the Dallas Townsend Extension Professional Enhancement
Award for his outstanding contributions in extension and outreach.

Gurpal Toor was appointed an Associate Editor of the Journal of Environmental Quality.

Jehangir Bhadha (Advisor, Jim Jawitz) was awarded the 2008 College of Agriculture and
Life Sciences Outstanding International Student Award.

Debolina Chakraborty (Advisor, Vimala Nair) was awarded third place in the 2008
Minority Student Poster Contest at the ASA/CSSA/SSSA International Annual Meetings
held Oct. 5-9 at Houston, TX.

Ryan Graunke, an undergraduate research student with Ann Wilkie and recent graduate
of SNRE/University of Florida, has won the Association for the Advancement of
Sustainability in Higher Education's 2008 "Student Research on Campus" Sustainability
Award for his paper: "Food and Fuel: Biogas Potential at Broward Dining Hall."

Jaya Das (Advisors, Samira Daroub and George O'Connor) was awarded first place in the
S-10 division poster competition at the 2008 Soil Science Society of America annual
meeting in Houston, Texas.

We are pleased to announce the arrival of twins, Julia and Melissa on June 22, 2008,
and to congratulate their proud parents Maria Silveira (SWSD) and Joao Vendramini
(Agronomy), Range Cattle REC, Ona.

Congratulations to PhD student Andrea Albertin and her husband on the birth of their
son Matthias on October 3rd, 2008. He is a delightful, happy, and healthy baby.

We would like to also congratulate PhD student Qin Lu and her husband on the birth of
their son Michael Zhang On December 2, 2008. Both mother and baby are doing well. .
Congratulations to the following students and staff for their outstanding
accompl ishments:
Frederick B. Smith Scholarship: Jared Sweat
Soil and Water Science Department Outstanding Undergraduate Award: Julie Ruh
William K. "Bill" Robertson Fellowship 2008-2009: Debolina Chakraborty, (Advisor .
Vimala Nair) and Shiny Mathews, (Advisor Lena Ma)
Victor W. Carlisle Fellowship 2008-2009: Victoria Gardner, (Advisor Mary Collins)
Sam Polston Memorial Fellowship 2008-2009: Alex Cheesman, (Advisors, Ramesh Reddy
and Ben Turner)
Bill Reve Superior Accomplishment Award: Brandon Hoover










In Memoriam William H. Reve

William H. Reve, Senior Laboratory Technician, Soil and Water Science
/ Department at the University of Florida, died in Gainesville, Florida on
November 15, 2008. He was born on September 2, 1954. He is survived
by his wife of 30 years, Kathy Reve and 17 year old son, Jeff Reve. Bill
worked as Senior Laboratory Technician for 30 years in the department.
fBill worked with Dr. Dean Rhue in managing the Soil Chemistry Core
Laboratory. Over the years, Bill helped many graduate students in
chemical analysis of their research samples. He was one of the most
dedicated staff members of the department. He will be missed by
S / faculty, staff, and students. To recognize Bill's service to the
S department, the SWSD Superior Accomplishment Award will named as Bill
I Reve Superior Accomplishment Award. Each year this award is given to
one staff member for their outstanding service to the department. Bill
was one of the past recipients of this award.



9th Annual Soil and Water Science Research Forum
The 9th Annual Soil and Water Science Research Forum http://soils.ifas.ufl.edu/forum/) was conducted on
September 12, 2008, in Gainesville, Florida. This year, Dr. Don Sparks, S. Hallock du Pont Chair and Chairperson,
Department of Plant and Soil Science, University of Delaware was the featured keynote speaker at the forum. We
thank all our sponsors (Florida Association of Environmental Soil Scientists, Hydromentia, Inc., DB Environmental
Labs, Inc) for their generous support of this year's forum. The forum showcased research programs for several
junior faculty members including: Carl Fitz (Ecological Modeling, Ft. Lauderdale REC); Patrick Inglett
(Biogeochemistry, Gainesville); Kelly Morgan (Nutrient Management and Modeling, Southwest Florida REC); Max
Teplitski (Microbial Ecology, Gainesville); Gurpal Toor (Urban Landscapes and Organic Contaminants, Gulf Coast
REC); and Alan Wright (Nutrient Management and Biogeochemistry, Everglades REC).
Congratulations to the following winners of the 2008 Annual Forum $500 research award.
Oral Presentation: Melissa Martin. Poster Presentations: Sylvia Lang, Jason Neumann, Alex Cheesman, and
Haryun Kim.
Please plan to attend the 10th Annual Soil Ft Water Science Research Forum September 11, 2009.


From our former students ...
Brian Murphy-
In 2001, I graduated from the Soil and Water Science department under the
Environmental Management in Agriculture Interdisciplinary Studies program with Dr.
Graetz as my advisor. As an undergrad, I was fortunate to have worked as an OPS Lab
technician for Dr. Ma and her post-doc, Dr. Tait Chirenje. Tait exposed me to the
wonderful world of GIS while assisting him on an urban arsenic soils study. Since then I
have immersed myself in the geospatial industry both at a academic level and through
my work with 3001 International, Inc.

I continue to reside in my hometown of Gainesville with my beautiful wife (and my dentist) Sara. For the past five
years, I have been working at 3001 International, Inc., now a wholly owned subsidiary of Northrop Grumman. As an
Area Director I am a part of their Business Development division where I report directly to the Senior VP. I travel
frequently across the U.S. to help uncover business opportunities with a variety of federal, state, and local
governmental agencies. One of our most recent "wins" of local interest was being selected by the St. John's River
Water Management District to provide them with 2009 updates to their digital orthophotography library, operating
with a budget of nearly $1.4 million.

I love my job, the people I get to meet and work with, and having the ability to work with imagery, LiDAR, maps, GIS
and photogrammetric products; I owe it all to having had such a great academic exposure through the Soil and
Water Science Department. Brian can be reached via email at bemurf@gmail.com




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