The National Ecological Observatory Network (NEON) is a project that monitors the effects of climate change, land use change, and invasive species on ecology across the United States. This document outlines NEON's science design for monitoring terrestrial microbial communities, including sampling soil, water, and sediment every 1-3 months to analyze microbial DNA and activity. Samples will be collected from over 100 sites and analyzed using DNA sequencing and other methods to understand changes in microbial populations and functions over time.

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The National Ecological Observatory Network is a project sponsored by the National Science
Foundation and managed under cooperative agreement by NEON Inc.

2. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
SCIENCE DESIGN FOR
TERRESTRIAL MICROBIAL
ECOLOGY AT NEON
Jacob Parnell

3. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Terrestrial Observation System (TOS) Field
Design
• Climate change
• Land-use dynamics
• Invasive species
• Biogeochemical cycles
• Biodiversity and ecosystem function
• Hydrological forecasting
• Infectious diseases and environment
Drivers of biological
and ecological change
Effects on organisms,
populations, and
communities
Responses
Drivers
Interactions,
Feedbacks

4. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Terrestrial Observation System (TOS) Field
Design

5. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Terrestrial Observation System (TOS) Field
Design
1012
Time [s]
100
103
106
109
1012
Length[μm]
100
10-3
103
106
109
Terrestrial & aquatic
field sampling
Terrestrial & aquatic
sensors
Airborne remote
sensing
Satellite and external
data
Metabolic processes,
CO2, O2, H2O exchange
Phenology,
productivity
Population dynamics, gas
and nutrient fluxes
Succession, biodiversity
Biogeochemical
cycles
Land surface interactions
500+ data products

6. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
What to measure & Frequency of measurements
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7. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
What to measure & Frequency of measurements
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For the first 2 years, samples will be
collected every month in order to
determine seasonal variation at each
site. Three time points will be selected
that maximize the seasonal variability
for the duration of the project.

8. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
What to measure & Frequency of measurements
Material 16S ITS Meta-
transcriptome
Meta-
genome
qPCR Cell count
Soil 5400 5400 5400 1800 5400 0
Water 324 324 324 108 324 324
Sediment 324 324 324 108 324 324
Benthic 324 324 324 108 324 324
Total/yr 6372 6372 6372 2124 6372 972
Total 19116
0
191160 191160 63720 191160 29160

9. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Spatial design:
org
Multiple Constraints Guide the Design
eptuneinc.org
was selected. strata a
• Classical ap
sample size
• Stratification
• Homogeneo
to determine
strata
• Generalized
Sampling to
probability b
• Complete sa
plot location
other invest
• Approach is
• Initial data c
design assu
refine calcul
number, allo
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Initial Data Collection for
Design Validation
Sequential ordering Reverse
Morton addresses
Randomized reverse
sequential ordering
Theobald
et al. 2007

10. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Spatial design:

11. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.

12. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Terrestrial Observation System (TOS) Field
Design
40m
40m

13. © 2012 National Ecological Observatory Network, Inc. ALL RIGHTS RESERVED.
Aquatic Observation System (AOS) Field Design

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Acknowledgements
Microbial Working Group:
G. King, L. Kinkel, L. Zeglin, C. Blackwood, N. Fierer, J. Gilbert
M. Allen, J. Tiedje, E. Triplett, D. Nemergut
Current/Previous NEON Scientists:
R. Gallery, K. Docherty, E. Hinckley, C. Meier, D. Barnett