SOUTHERN SIERRA CRITICAL ZONE OBSERVATORY - KREW
PROJECT REQUEST FORM
Project Director/Principal Investigator (include contact information):
Emma Aronson
Collaborators:
Stephen Hart
Project Title:
Impact of biotic and abiotic aeolian inputs in terrestrial ecosystems
Project proposal
Objectives:
Everything is not everywhere, but the environment does select. Just like
macroorganisms, microorganisms require vectors for dispersal, although comparatively
less is known about the role of microbial dispersal in the functioning of terrestrial
ecosystems (Martiny et al. 2006, Green et al. 2008, Fierer 2008). Similarly, the
significance of aeolian inputs of nutrients for the maintenance of primary production has
only been evaluated for a few ecosystems (Swap et al. 1992, Chadwick et al. 1999, Neff
et al. 2008). In addition, there has been growing interest in aeolian input of black carbon
(C) to soils as a potential long-term sink for C, as well as a mechanism for improving soil
fertility (Schmidt and Noack 2000, Forbes et al. 2006, Liang et al. 2006). The
simultaneous analysis of aeolian particles and microorganisms should contribute insight
on the significance of wind transport as a vector for microbial dispersal and soil
improvement (Smith 2013). We propose to quantify the input of microorganisms and
particles to a variety of contrasting terrestrial ecosystems, as well as assess the
significance of these inputs to the development of soil fertility and microbial
communities. We will address these issues in a three-phase research project. The first
phase will use a suite of measurement techniques to characterize the microorganisms,
nutrients, and black C entering contrasting terrestrial ecosystems along an altitudinal
gradient that comprises the Southern Sierra Critical Zone Observatory (SSCZO). Further,
geochemical tracers will be used to determine the likely geographical origins of the
particles and particle-attached microorganisms entering these ecosystems. The four sites
to be sampled (oak savannah, pine/oak forest, mixed-conifer, and subalpine forest) all
have eddy-covariance towers that will be used to actively collect aeolian samples. Passive
samplers (“dust traps”) will also be installed at each site, and soil profiles will be sampled
to characterize the existing microbial communities, nutrient and black C pools, and for
estimating long-term rates of dust deposition using geochemical tracers. The second
phase will be experimental, and involve the removal of intact soil cores from each
location, sterilization of the cores, and then replacement of the cores to their original
locations. These soil cores will serve as novel substrates for colonization by the aeolian
or nearby soil communities, and will be sampled periodically to determine the similarity
of the novel microbial communities to both sources of genetic material. The third and
final phase of this project will involve collaborators at other sites where existing eddy
covariance towers exist (including other CZOs, AmeriFlux sites, new NEON sites, and
LTER sites). We will lead a coordinated effort to sample the aeolian particles and soil
microbial communities at a subset of these sites across the US. Sites will be selected to
provide a broad range in climate and soil type to evaluate the potential role of these
factors on microbial dispersal and aeolian particle inputs. The data gathered from this
project will be shared openly and will have lasting ramifications for our understanding
about soil microbial community assemblage and transport vectors, as well as the role of
aeolian inputs on soils.
Rationale and Significance:
The diverse community of bacteria and archaea in the soil are vital to ecosystem
processes. Microorganisms are also important regulators of plant community dynamics
and diversity (Van der Heijden et al. 2008). Studies showing the negative impacts of
invasive animal and plant species, and even fungi, on the populations of their native
counterparts are becoming common (Litchman 2010). However, the general possibility of
invasive non-pathogenic microorganisms has not been thoroughly addressed in terrestrial
ecosystems, despite an increasing number of putative invasions (Griffin et al. 2002,
Litchman 2010). Beneficial microorganisms, such as nitrogen-fixing bacteria,
mycorrhizal mutualists, and rhizosphere colonists, could colonize terrestrial ecosystems
via aeolian transport and positively impact ecosystem functioning. The relative
importance of dispersal limitations versus environmental filtering in community
assembly across whole ecosystems and regions has received much attention for
macroorganisms (Ozinga et al. 2005, Lebrua-Trejos et al. 2010). However, the
comparative influence of these filters on microbial community assembly is largely
unclear (Kivlin et al. 2011). Determining assembly rules is critical for microorganisms
(Fukami et al. 2010), as interactions between microbial taxa can alter important
ecosystem processes such as net primary productivity, decomposition, and nutrient
cycling rates (Bell et al. 2005, Ayers et al. 2009, Bradford and Fierer 2012).
The basic tenet of microbial ecology for more than 70 years had been that “everything
is everywhere, but the environment selects” (Baas Becking 1934). However, as molecular
techniques surpassed morphological approaches, they have redefined microbial
phylogenies and biogeography (Rout and Calloway 2012). These techniques, particularly
high-throughput metagenomic sequencing, allow identification of separate species in
diverse communities and complex ecosystems. The recent application of these techniques
has demonstrated that, similar to macroorganisms, there is a spatial patterning of soil
microorganisms at local and regional scales. As with larger organisms, dispersal
limitations, environmental filters, and the resistance of native communities to invasion all
likely contribute to these patterns (Martiny et al. 2006, Green et al. 2008).
Very few studies have investigated microbial transport, with little information in the
literature on vectors for microbial dispersal (Smith et al 2012, Creamean et al. 2013,
Smith 2013). There is a growing body of evidence showing that aeolian processes interact
with ecosystems at multiple scales, contributing to important biophysical feedbacks
between the biotic and abiotic components of the earth (Ravi et al. 2011). Wind is often
characterized as a dispersal vector of particles such as dust (Chadwick et al. 1999, Neff et
al. 2008) and black C (Forbes et al. 2006), but the co-migration of microorganisms either
free of or attached to these particles has only recently been acknowledged and has not
been studied to date (Smith 2013). These invasive aeolian microbes and co-transported
particles have the potential to greatly influence native soils and the microbial
communities present.
Our previous work within the mixed-conifer site of the SSCZO suggests that aeolian
inputs may play a significant role in regolith formation and nutrient cycling in the
SSCZO (Hahm and Riebe in prep.), thus being an important, yet unmeasured contributor
to critical zone processes. Additionally, recent studies have suggested that long-range
transport of black C (Forbes et al. 2006) and microorganisms (Smith et al 2012,
Creamean et al. 2013, Smith 2013), in addition to particulate nutrient inputs (Chadwick et
al. 1999, Neff et al. 2008, Coble et al. in prep.), can be significant. Additionally, particles
co-transported with microorganisms in aerosols can suggest the geographic origin of cells
and how long they have been aloft in the atmosphere (Smith 2013). These materials and
organisms may be important contributors to soil development, particularly in poorly
developed soils (Forbes et al. 2006, Lepleux et al. 2012).
We propose to evaluate contemporary aeolian inputs across the entire elevation
transect (4 sites), using a combination of active and passive samplers. Active samplers
(Goossens and Offer 2000, Brodie et al. 2007) will be placed above the tree canopy,
attached to existing eddy covariance towers, while passive samplers (“dust traps”; Reheis
2003, Coble et al. in prep.) will be located 2 m aboveground (to prevent any saltation
inputs) within canopy gaps. Collected dust will be analyzed for nutrient content,
geochemical tracers (Chadwick et al. 1999, Reynolds et al. 2012, Coble et al. in prep.),
black C (Forbes et al. 2006), and microbial communities (Brodie et al. 2007, CruzMartínez et al. 2012). These data will provide information on contemporary inputs of
aerosols, both biotic and abiotic, and the potential geographic sources of these particles.
The aeolian microbial community composition will be analyzed and compared to samples
collected in surficial soil horizons in order to determine the fraction of the microbial
community entering the soil on the wind. Deeper soil horizons will also be assessed to
estimate long-term rates of particulate deposition using geochemical tracers. These data
will elucidate the role of allochtonous inputs, both biotic and abiotic, on critical zone
processes in the SSCZO.
Research Questions:
Does wind act as a significant vector of dispersal for soil microorganisms and nutrients?
Sub-question 1) What relative role do neighboring soil and incoming aeolian
microorganisks have in colonizing novel substrates? We hypothesize that the soil
bacterial, archaeal and fungal communities will be similar to the wind dispersed
communities, but that environmental filtering and legacy effects will play a lesser role in
soil community assembly relative to dispersal constraints.
Sub-question 2) If we can show that wind dispersed, aerosol-attached or free-living
aeolian microorganisms are important for shaping extant soil microbial communities,
what relevance does that have for ecosystem functioning? We hypothesize that using
metagenomic sequencing of functional genes, we will find that aeolian microorganisms
are contributing functional diversity to the soil community.
Sub-question 3) What role do the incoming aeolian nutrients and black C have in soil
development across contrasting terrestrial ecosystems? We hypothesize that
contemporary and long-term particulate nutrient and black C inputs will contribute
significantly to soil development in all of these ecosystems. However, we predict that
relative importance of these allochtonous to residual soil development and fertility will be
greatest at higher elevations where soils are less developed (subalpine forest), and wind
transport and particulate impaction are likely greatest.
Experimental Plan:
We aim to test the relative importance of dispersal limitation versus environmental
filtering on soil microbial community composition in the SSCZO and at selected sites
across the U.S. In addition, we will quantify simultaneously the abiotic component of
these aerosols in order to estimate nutrient and black C inputs to these ecosystems, as
well as indicate the possible origin of cells and how long they have been aloft in the
atmosphere. The project will consist of three main phases: 1) an intensive investigation of
contemporary inputs of the biotic and abiotic aerosol components at the four ecosystem
types of the SSCZO, and comparisons with extant soil pools; 2) a soil colonization
experiment at these same sites where the recolonization of sterilized, intact soil cores will
be studied across these same four sites; and 3) an extensive, collaborative biogeography
project including other existing eddy covariance tower sites across the U.S., including
other CZOs, AmeriFlux towers, NEON sites, and LTERs.
Study site: Phases 1 and 2 of this proposed research will be conducted within the
Southern Sierra Critical Zone Observatory (SSCZO), a community platform for research
on critical-zone processes across the rain-snow transition zone in the southern Sierra
Nevada (http://criticalzone.org/sierra/). Dr. Hart is a co-PI on the project and Dr. Aronson is a
project collaborator. The SSCZO is part of a national network of 10 sites (4 new sites
were added in 2014) for investigating Earth’s critical zone, where the constantly evolving
boundary layer of rock, soil, water, air, and living organisms interact
(http://criticalzone.org/national/). In the SSCZO, there are four eddy covariance flux towers
located along an altitudinal gradient (400 – 2700 m.a.s.l.) across the rain-snow transition
zone. The towers extend from the ground to above the tree canopy within 4 contrasting
terrestrial ecosystems: oak savannah, pine/oak forest, mixed-conifer forest, and subalpine
forest. Detailed micrometeorological data (including high-temporal resolution 3-D wind
velocity and direction, precipitation, temperature, etc.) are collected at each tower. These
data are currently used to estimate exchanges of energy, water, and carbon dioxide
between the biosphere and the atmosphere (Goulden et al. 2012). The existing towers,
environmental sensors, and surrounding undisturbed soils along this environmental
gradient provide an ideal platform for the study of co-transport of microorganisms and
abiotic particles by wind, and their impact on the functioning of terrestrial ecosystems.
Intensive soil and wind biotic and abiotic assessment in the SSCZO. We propose to
evaluate contemporary aeolian inputs across the entire altitudinal transect of the SSCZO
(4 sites), using active samplers and passive samplers. The sites along this transect differ
in vegetation structure, soil development on a common parent material (granitic
residuum), wind velocities, air temperature, precipitation type and amount, and length of
dry season. These vegetation, soil, and climatic differences should provide strong
contrasts in the extant soil microbial communities and the biotic and abiotic aerosol
inputs to these ecosystems. Previous work at the SSCZO mixed-conifer site suggests that
aeolian inputs may play a significant role in regolith formation and nutrient cycling
(Hahm and Riebe in prep). We will use the existing, continuous air-sampling system of
the eddy covariance towers (sampled above the plant canopy) for our active aerosol
samplers (Brodie et al. 2007). Currently, 1µm filters are used to minimize contamination
of the InfraRed Gas Analyzer flow cell. During sampling, a second filter with a 0.22 µm
pore size will be added downstream of the existing filter. This will allow us to capture
both larger and smaller particulates. In both cases, sterile filters will be used and replaced
at set intervals. These filters will be analyzed for elemental composition (Chadwick et al.
1999), black C (Forbes et al. 2006), and microbial communities (Brodie et al. 2007).
Furthermore, whenever filters are exchanged, composite soil samples (O and upper A
horizons) will be collected within the “footprint” of each tower to compare the extant soil
microbial communities and nutrient and black C pools with aeolian inputs. We will also
deploy multiple passive dust samplers (Reheis 2003, Coble et al. in prep) within open
areas of each tower’s footprint to further characterize the abiotic aeolian inputs to these
ecosystems. These data will elucidate the role of allochtonous inputs, both biotic and
abiotic, on critical zone processes within the SSCZO.
Microbial community profiling of air and soil samples will be performed via DNA
extraction followed by polymerase chain reaction (PCR) and quantitative PCR (qPCR) of
target genes. The genes chosen include the combined 16S rRNA genetic region for
bacteria and archaea (Degnan & Ochman 2012; Aronson et al. 2013), and the ITS2 region
for fungi (Ihrmark et al. 2012), and key biogeochemical genes, including pmoA for
methane oxidation, mcrA for methane production (Aronson et al. 2013), narG, nirS, nirK,
and nosZ denitrification genes, amoA for the ammonia oxidation step of nitrification and
nifH for nitrogen fixation. The PCR extracts will be sequenced using the Illumina MiSeq
system, one of which is now owned by both UCR and UCM. Quantification of variability
will be assessed using Quantitative Insights Into Microbial Ecology (QIIME).
Broader Impacts:
This project will contribute to NSF goals of advancing discovery and understanding,
bringing together interdisciplinary knowledge, and promoting teaching and training of
early career faculty, students, and young scientists. The PI, Dr. Aronson, is a recently
hired assistant professor with no previous federal funding as a standard grant. Both UCR
and UCM, where the PI and Co-PI are faculty members, are Hispanic-serving institutions
(the only two within the 10-campus UC system) with the highest percentage of
underrepresented students of all the UC campuses. A female, under-represented minority
graduate student currently works in the Aronson lab, and two minority undergraduate
students (1 male, 1 female) currently work in the Hart lab. We will continue to recruit and
train minority undergraduates as part of this project, and these undergraduates will be
involved in every phase of the research (field, lab, data analysis, and writing). By
associating our project with the SSCZO as well as other CZOs and federally funded
network projects, we can take advantage of the existing and extensive outreach activities
offered by these programs. For instance, the SSCZO has an outreach coordinator
(http://criticalzone.org/sierra/education-outreach/) that will assist us in communicating our results to
local K-12 schools, stakeholders interested in forests management, and the local foothill
and mountain communities surrounding our study sites. We expect our research project to
directly support the training of ≥10 undergraduate students, 2 graduate students, and a
postdoctoral researcher. The career development of the postdoctoral researcher will be
enhanced through a mentoring program designed to provide postdoctoral researchers with
the skills and experience to prepare them to excel in their careers. Further, our
collaborative biogeography experiment will improve scientific network infrastructure by
bringing together research scientists and students involved in numerous federally funded
sensor networks currently running across the U.S., as well as provide opportunities for
cross-institution exchanges (e.g., https://criticalzone.org/sierra/research/cross-czo-studies-sierra/).
Describe the project location (attach map if necessary):
Within 10M circle around base of towers at each tower site.
Duration and period of use:
From March 2014 through February 2015
Describe any markers, including tags, flagging, stakes, fencing, or other to be used:
None.
Will other USFS facilities or resources be needed? X Yes ☐ No
If Yes, please describe:
We have already booked 2 nights in the SJER dormatory.
Do you intend to publish your results? X Yes ☐ No
If Yes, please remember to cite necessary parties (ex. SSCZO, KREW, etc.)
If implementation of your project includes use of humans as experimental subjects
or radiation, biological, or toxic chemicals, please explain.
Please provide the required proof of liability insurance, or fill out the necessary UC
Merced liability waiver form before accessing research site.
Liability waivers will be attached.
I will provide annual progress reports, electronic copies of all published reports, and a
final report at the end of the study. I agree to remove all study markers and equipment at
the end of the study. I also plan to adhere to the SSCZO data policy.
____
__________3/25/14__________________
_______________________
Project Director/Principle Investigator
Date
APPROVAL SIGNATURES
________________________________
______________________
Matthew Meadows
Date
SSCZO Hydrologist
Sierra Nevada Research Institute, UC Merced
USFS Forestry Sciences Lab
2081 E. Sierra Avenue
Fresno, CA 93710
559-323-3218 (o)
209-233-2802 (c)
mmeadows@ucmerced.edu
________________________________
Roger Bales, PhD
Director
Sierra Nevada Research Institute
University of California Merced
5200 N lake Rd
Merced, CA 95343
209-228-4348
rbales@ucmerced.edu
_______________________
Date
APPROVAL FOR USAGE OF KREW-PSW RESOURCES OR FACILITIES
________________________________
Carolyn Hunsaker, PhD
Research Ecologist
USFS Forestry Sciences Lab
2081 E. Sierra Avenue
Fresno, CA 93710
559-323-3211
chunsaker@fs.fed.us
______________________
Date
SUBMIT THIS FORM TO MATTHEW MEADOWS
Distribution: M. Meadows, R. Bales, C. Hunsaker.
Rev 11/12