Investigating the role of microbial composition in soil formation within the Critical Zone
Background and Project Description:
The Critical Zone (CZ) is the thin, near surface environment that extends from the top of
vegetation down to groundwater. The CZ hosts complex interactions involving rock, soil, water, air and
living organisms that regulate the natural habitat. This layer determines the availability of life-sustaining
resources such as food production and water quality (NRC, 2001). Critical Zone Observatories (CZO)
have been established globally to form a network that aims to
quantify the interactions between rocks and life in a consistent and
comparable manner to help sustainably manage our valuable
natural resources. Representing a thin section within the CZ is soil.
Soil loss is a major issue facing humanity as it is essential for food
production and other immensely important resources (Banwart,
2011). In addition, global temperatures are anticipated to rise in
future years, therefore studying the influence of climate on soils
will help us predict how climate change will impact the CZ.
To investigate the influence of climate on soil properties,
study sites in North America, Puerto Rico and Wales were
established and added to the Susquehanna Shale Hills CZO in
central Pennsylvania (Dere et al., 2013) (Fig. 1). Study sites vary in
mean annual temperature (MAT) and precipitation (MAP) from
cold and wet in the north to warm and wet in the south. All sites are
underlain by shale, which is an abundant sedimentary rock on
Earth. Soil cores were collected from the surface to bedrock, or as
Figure 1. Map showing the North
deep as possible, on the ridgetops of each site. The cores were
American shale sampling sites.
evaluated for geochemistry, mineralogy and physical properties and DNA from soil samples collected
compared across the sites. Initial findings show that soils are deeper from PA, VA, TN and AL this
and more weathered in warmer and wetter climates (Dere et al.,
past summer will be extracted and
2013; Dere et al., 2016). Further data would improve our
analyzed for microbial
understanding of the role climate plays in soil formation and
composition.
weathering processes, particularly from a variety of climates, and at
a global scale.
Another significant component that would help us understand the influence of climate on soil
properties would be to investigate microbial composition. Microbes are vital for driving a variety of
weathering processes either directly or indirectly through their activities. For example, microbes can
directly change iron oxide minerals by oxidizing iron or indirectly accelerate rock weathering by
decomposing organic carbon to produce carbon dioxide and organic acids, causing soil acidification and
then mineral dissolution (Amundson et al., 2003). The composition and function of microbial
communities is known to change with different environmental variables (Fierer et al., 2006; Lozupone et
al., 2007; Rousk et al., 2010), which can be expected to change across soil horizons and with depth.
However, most studies have focused only on the upper 0-10 cm of soil (Eilers et al., 2012) and have
neglected to evaluate the changes in microbial community composition with depth and how this may
affect their function. Here, I propose to examine samples collected across a shale weathering gradient
(resulting in soils of different depth) to identify microbial community composition with depth and
identify potential changes in microbial community function in response to resource availability (such as
organic carbon or iron).
Methods:
In August of 2016, I was part of a team led by Dr. Dere and Dr. Santini from the University of
Queensland that traveled to the North American Shale Transect sites to collect soil samples from the
ridgetop experiment sites. Since samples from these sites have already been evaluated for geochemistry,
mineralogy and physical properties (Dere et
al., 2013; Dere et al., 2016), the main
objective of the new samples is to analyze
microbial composition and function with
depth. Our goal is to determine the microbial
composition, including archaeal, bacterial, and
fungal species present, in shale derived soils
across the climosequence of the Shale
Transect. The work involved digging up to
Figure 2. Map showing the new shale sampling location
1.5 m deep pits and collecting samples in
100 km southwest of Brisbane, Australia.
each horizon while maintaining a clean and
sterile environment by wearing nitrile gloves and sterilizing all tools and sampling tubes with ethanol.
The samples are preserved with LifeGuard! Soil Preservation Solution and have been kept frozen until
we are able to begin analysis. The next step is to extract the DNA from the samples using PowerSoil
DNA Isolation Kits and send the samples for DNA sequence analysis (16S rRNA amplicon sequencing at
the Australian Centre for Ecogenomics, University of Queensland).
Dr. Santini is a soil scientist and geomicrobiologist at the University of Queensland, Australia.
She will provide her expertise in DNA extraction, sequencing, and bioinformatics techniques (Santini et
al., 2016). Dr. Santini leads the Biogeosciences Research Group (BiGS) at the university where they have
the equipment to perform microbial analysis. Australia also presents an exciting opportunity to collect
new samples at a shale site near Mt. Barney, approximately 100 km southwest of Brisbane (Fig. 2). Shale
here is geochemically similar to the previously studied shale in North America, but presents a subtropical
environment in the southern hemisphere. The timing of the new sample collection (February 2017) is late
summer in Australia, similar to the seasonal timing in which the North American shale microbial samples
were collected. This will help ensure seasonal differences in microbial composition are avoided. The
process to collect new soil samples near Mt. Barney will be identical to the previously collected North
American samples. We will dig a pit 1.5 m deep and collect samples from each horizon while maintaining
a sterile environment. The new samples from Australia will also undergo DNA extraction using
PowerSoil! DNA Isolation Kits followed by sequencing. In addition, all soil samples from the North
American and Australian study will be ground and sent for analysis at the Pennsylvania State University
Materials Characterization Lab. Geochemical data will allow us to identify the drivers of microbial
community composition with depth and climate across the North American and Australian shale sites.
Ultimately, this study will help us understand how different climates are impacting shale soil formation
and how microbial composition at depth may enhance or decrease weathering rates.
Project Timeline:!
February 2017
March 2017
April 2017 – Aug. 2017
Sep. 2017 – March 2018
Travel to Brisbane, Australia; collect new samples, extract DNA
Send soil samples for geochemical analysis
Analyze DNA and geochemical data
Submit abstract, FUSE report and present at Student Research Fair
Student/Faculty Mentor Roles:
I have worked closely with Dr. Dere since starting school at UNO and am very interested in CZ
research, especially the process of sampling for microbial composition. I have experience collecting these
samples at three of the U.S. CZ Observatories this past summer, and will be able to follow the process
further by testing and analyzing them with help from Dr. Dere and Dr. Santini. Dr. Santini will provide
me with geomicrobiology knowledge and training for DNA extraction and sequencing along with how to
interpret the results. Dr. Dere will provide support for writing and presenting results and help interpret the
geochemical data.
Budget Justification:
Budget Item
International Travel
Airfare roundtrip Omaha, NE to Brisbane, Australia February 11-26
Visa
Lodging (provided by Dr. Santini, Univ. Queensland)
Local Transport (provided by Dr. Santini, Univ. Queensland)
Project
PowerSoil® DNA Isolation Kit
Lifeguard® Soil Preservation Solution
Geochemical Analysis ($33/sample; 35 samples total)
Organic Carbon Analysis ($7/sample; 35 samples total)
Stipend
Cost
$1975
$25
$0
$0
Total $2000
$515
$210
$1155
$245
$375
Total $2500
Total amount requested $4500
I am requesting a total of $4,500 to investigate the role of microbial community composition in
soil formation within the Critical Zone with Dr. Dere at the University of Nebraska at Omaha and Dr.
Santini at the University of Queensland in Brisbane, Australia. $2,000 of the funds will support travel to
Brisbane, Australia in February 2017 where I will meet Dr. Santini at the University of Queensland. Dr.
Santini has generously offered transport for the collection of new samples near Mt. Barney and DNA
extractions of all samples at the university labs. She has also graciously offered that I could stay at her
home during the trip, meaning no funds are requested for lodging and transportation expenses. I have also
requested a stipend of $375 to cover the cost of meals, estimated at approximately $23/day for sixteen
days.
To facilitate the completion of the research objectives, funds have also been requested to
purchase PowerSoil! DNA Isolation Kits ($515) to analyze microbial composition and Lifeguard! Soil
Preservation Solution ($210), to preserve new samples collected near Mt. Barney. Soil chemistry analysis
at $33/sample for 35 samples is requested for total elemental geochemical analysis which will to be
completed at the Pennsylvania State University Soil Characterization Lab (State College, Pennsylvania).
Finally, $7/sample for 35 samples is requested for soil organic carbon analysis at Ward Laboratories
(Kearney, Nebraska).
Funding requested here would enable both travel and completion of the initial research objectives
outlined in the project proposal.
References:
Amundson R., Guo Y., and Gong P. (2003) Soil diversity and land use in the United States. Ecosystems
6: 470-482.
Banwart, S.A. (2001) Save our soils. Nature 474:151-152.
Dere, A.L., White T. S., April R. H., and Brantley S. L. (2016) Mineralogical transformations and soil
development in shale across a latitudinal climosequence. Soil Sci. Soc. Amer. J. 80:623-636.
Dere, A. L., White T. S., April R.H., Reynolds B., Miller T. E., Knapp E. P., McKay L. D. and Brantley
S. L. (2013) Climate dependence of feldspar weathering along a latitudinal gradient. Geochim.
Cosmochim. Acta. 122:101-126. doi: 10.1016/j.gca.2013.08.001
Fierer N., Jackson R. B. (2006) The diversity of biogeography of soil bacterial communities. Proc. Natl.
Acad. Sci. 103:626-631.
Eilers, K. G., Debenport S, Anderson S, and Fierer N. (2012) Digging deeper of fine unique microbial
communities: the strong effect of depth on the structure and bacterial and archaeal communities
in soil. Soil Biol. Biochem. 50:58-65.
Lozupone C., and Knight R. (2007) Global patterns in bacterial diversity. Proc. Natl. Acad. Sci.
104:11436-11440.
National Research Council (NRC) (2001) Basic Research Opportunities in Earth Science. National
Academy Press, Washington, 154 p.
Rousk J., Baath E., Brookes P. C., Lauber C. L., Lozupone C., Caporaso J. G., Knight R., and Fierer N.
(2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J.
4:1340-1351.
Santini T. C., Malcolm L. I., Tyson G. W., Warren, L. A. (2016) pH and organic carbon dose rates control
microbially driven bioremediation efficacy in alkaline bauxite residue. Environ. Sci. Tech. doi:
10.1021/acs.est.6b01973
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October 6, 2016
Dear FUSE Proposal Committee,
I am writing to express my support of Sara Parcher’s FUSE proposal. Sara is currently a second year geology
student in the Department of Geography/Geology at UNO. I first had the pleasure of working with Sara in my Fall
2015 semester Introductory Physical Geology course and she was an outstanding student in the classroom. She
displayed a great aptitude for learning and completed all assignments on schedule and with high quality. Despite
completing only one geology course, Sara wasted no time in applying for, and obtaining, an Iowa EPSCoR summer
research internship working at the University of Iowa on soil hydrology research. She thrived in the research
environment, completing and presenting a research project investigating slope aspect differences in shallow soils
under agricultural land management. Following the completion of the summer internship, Sara joined my research
team for a week of intensive field work in the Appalachian Mountains. Field conditions were some of the more
difficult I have experienced, with high heat and humidity, intermittent rain, labor intensive soil pit excavation, and
hiking with sample- and gear-laden packs. Sara did not complain and was up to the challenge each day, providing a
much needed boost in morale. She also took advantage of every opportunity to learn a new technique or ask
questions about the research methods or interpretations. Sara is eager to continue the research she began this summer
and has taken the initiative to develop and submit this FUSE proposal.
The construction of this FUSE proposal has been highly collaborative, with the initial ideas germinating from
discussions while conducting fieldwork this past summer. Sara is especially interested in helping complete the
microbial analysis of soils she collected with the research team this summer but she is also proposing to collect
additional samples in Australia that would expand the dataset on comparable shale soils in the southern hemisphere.
The proposed project is related to my research activity and would greatly complement my studies on soil formation
in various climates. I do not, however, have the expertise to guide her in microbial research efforts so she will work
with Dr. Talitha Santini, from the University of Queensland in Australia, to learn additional techniques necessary to
complete the project. Dr. Santini has the research facilities and expertise to mentor Sara in the laboratory while my
role will focus more on helping her write up and present her findings when she returns from Australia. The proposed
work would fill a knowledge gap in our understanding of how microbial communities differ with depth and as a
function of climate and contribute data to a larger international effort to understand how life and rock interact in the
Critical Zone.
I am confident that Sara has the skills to succeed in this project. She is self-motivated and driven by an
intense curiosity to understand earth systems but is also detail oriented, careful and deliberate, all of which instill
confidence in her ability to conduct high quality research. Sara is an excellent student and promising researcher. She
is still new to research and geology, but has shown incredible ambition and a desire to learn. I am excited about her
proposed work and willing to provide the mentoring and support to ensure she is successful in this endeavor. I thank
you for considering her proposal and please do not hesitate to contact me if you have any further questions.
Sincerely,
Ashlee Dere
Assistant Professor of Geology
Department of Geography/Geology
University of Nebraska – Omaha
Omaha, NE 68182
(402) 554 – 3317
[email protected]
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The University of Nebraska at Omaha shall not discriminate based upon age, race,
ethnicity, color, national origin, gender-identity,sex, pregnancy, disability, sexual
orientation, genetic information, veteran's status, marital status, religion, or political
affiliation.
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School of Geography,
Planning and Environmental
Management
Dr Talitha Santini, PhD, BSc
(Hons), BA
Senior Lecturer,
Environmental Management
CRICOS PROVIDER NUMBER 00025B
9 October 2016
To whom it may concern,
RE: Support for FUSE grant application, Sara Parcher
I would like to express my strong support for the research project proposed by Sara Parcher,
supervised by Dr Ashlee Dere, to be completed within the School of Geography, Planning, and
Environmental Management at the University of Queensland (UQ), Australia in 2017. This
proposal has been developed through a research collaboration between myself and Dr Dere, for
which we recently completed a week-long field trip along the Appalachian Mountains with four
UNO students including Ms Parcher. I was impressed by Sara’s interest and knowledge of soil
weathering and development during this trip, and I believe that Sara shows substantial promise
as a researcher.
Sara’s proposed work would fill in a crucial knowledge gap in our understanding of shale
weathering across an international climate gradient, by providing the first insights into the
composition and potential roles of microbial communities in controlling weathering rates. Sara
would be travelling to my laboratory at UQ to acquire skills in microbial analysis and analyse
recently collected samples plus another set to be collected from our Australian site (Main Range
Critical Zone Observatory, south-east Queensland) during her visit.
Our School will provide access to our field equipment, office, laboratory facilities as an in-kind
contribution to this project. I will personally train and supervise Sara during her visit, and
facilitate and assist with field work. Sara will also have the opportunity to network with other
research students and staff across Schools and research Institutes at UQ including the School
of Earth Sciences, the School of Agriculture and Food Sciences, the School of Chemical and
Molecular Biosciences, the Centre for Microscopy and Microanalysis, and the Sustainable
Minerals Institute.
I would be delighted to host Sara Parcher’s research visit, and I look forward to building our
fruitful research collaboration with the University of Nebraska at Omaha.
Sincerely,
Talitha Santini
Senior Lecturer (Associate Professor)
School of Geography, Planning, and Environmental Management
The University of Queensland
School of Geography, Planning and
Environmental Management
Level 4, Chamberlain Building (35)
Campbell Drive
St.Lucia
The University of Queensland
Brisbane QLD 4072 Australia
T +61 7 3365-6455
F + 61 7 3365 6899
E [email protected]
W www.gpem.uq.edu.au
CRICOS PROVIDER NUMBER 00025B