Internship Project: Successional Changes in Soil Microbial Communities in a Northeastern US
Hardwood Forest
Nicole Dear (Senior, University of Michigan), Jacob Parnell (NEON)
Motivation
N fixation
N fixing bacteria community shift
25%
10%
Organism abundance analysis used 16S rRNA data and MGRAST (mRNA) best hit classification. Community information
from the different stages was compared to determine if
succession had a significant impact on soil microbial
community structure and function. Statistical (ANOVA, cluster
based analyses) and trend analyses were used to provide
insight into how soil microbial communities respond to
disturbance and change with succession.
0.4%
0.14%
0.4%
0.12%
0.3%
% gene expression
15%
0.10%
0.08%
0.06%
5%
0%
Disturbed
Successional
0.1%
0.00%
0.0%
Successional
Mature
Trehalose Biosynthesis (p=.033413)
0.2%
0.02%
Disturbed
Pentose phosphate pathway (p=.040735)
0.2%
0.1%
Mature
Entner-Doudoroff Pathway (p=.004897)
0.3%
0.04%
Shift from free living N fixing bacteria (Actinobacteria,
Green Sulfur Bacteria) in disturbed stage to rhizobium
(Proteobacteria) in mature stage. Note: Green Non-sulfur bacteria do
Disturbed
Successional
Mature
Activity of genes associated with rhizobium high in
mature successional stage2
Activity of genes associated with free living N fixers
high in disturbed successional stage
not fix N, but were included in analysis because both Green sulfur and non-sulfur bacteria have
chlorosome gene.
Decrease in nitrifiers and inhibition
N cycle bottleneck and C accumulation
of nitrification (pH<5)
40
0.6%
Pearson1
N (%)
Crenarchaeota (p=.02052)
35
Nitrospirae (p=.004715)
0.5%
Nitrification
C (%)
30
% abundance
0.4%
25
0.3%
%
20
15
0.2%
10
0.1%
5
0
0.0%
Pearson1
Disturbed, pH 5.6
Successional, pH 5.1
Disturbed
Mature, pH 3.7
Discussion
Future Research
•  A bottleneck in the N cycle causes inhibition of
nitrification and a buildup of C in mature soils;
temperature forests act like C sinks.
•  Disturbed sites act like C sources, as disturbances
reset the process of succession and allow
nitrification to occur.
•  Mild frequent disturbance such as climate change
could likely cause a feedback loop, constantly
resetting the process of succession and preventing
soils from accumulating C.
Control:
Measure nitrification in different successional stages
•  Nitrification should be inhibited in mature forest plots/
not inhibited in disturbed plots
•  Does inhibition correspond to a decreased abundance
of nitrifiers?
Experiment:
1.  Lower pH in a disturbed site
2.  Raise pH in a mature forest site
•  Is nitrification inhibited?
•  Does soil C increase?
Successional
Mature
Previous studies show that when nitrification is inhibited in temperate
forests, a bottleneck occurs in the N cycle and C accumulates in the
soil4; mature soils experienced increased % N and C
Low soil pH in mature successional stage correlated to a
decreased abundance of nitrifying bacteria and archaea;
nitrification is inhibited in soils with pH less than 53
Methods
Soil samples were taken from ten of twenty
randomly located 20m x 20m plots
containing four 10m x 10m subplots at
three successional stages (disturbed,
successional, mature). Microbial DNA/ RNA
was extracted from soil samples, purified,
amplified and sequenced.
0.16%
20%
0.5%
Carboxysome (p=.009196)
Chlorosome (p=.05970)
Cytochrome B6-F complex (p=.008581)
Proteobacteria (p= .03026)
Site Description
Mature forest
Actinobacteria (p=.01861)
Green Sulfur/ Non-sulfur (not N fixing) Bacteria (p=2.7635e-5)
Soil microbial community samples were collected at three
successional stages (disturbed, successional, mature)
from a mixed northern hardwood site at Harvard Forest.
Microbial community data was compared to determine if
succession impacted community structure and function.
Statistical and trend analyses provided insight into how
soil microbial communities respond to disturbance, and
ultimately how these responses influence the ecosystem
processes they drive.
Soil microbial community samples
were collected from ten plots at three
successional stages from Harvard
Forest and Quabbin Reservoir
research area in July 2012. Mean site
temperatures range from -7°C to
20°C with a mean annual
precipitation of 110cm.
Successional stages:
1. disturbed grassland
2. successional shrubland
3. mature forest: red oak (Quercus
rubra), red maple (Acer rubrum),
black birch (Betula lenta), white pine
(Pinus strobus) and eastern hemlock
(Tsuga Canadensis).
Shift in activity of genes associated with N fixing bacteria
0.18%
% gene expression
terrestrial ecosystems driving many key processes such
as nitrogen (N) fixation and carbon (C) sequestration.
Despite the importance of soil microbial communities, little
is known about how they respond to disturbance and
change with succession. Understanding soil microbial
community succession is vital to understanding
ecosystem functioning. The National Ecological
Observatory Network (NEON) monitors causes and
responses of changing ecosystems on a continental scale
and provides a platform to address these concerns.
% abundance
Author:
Leslie
Goldman
Soil microbial
communities
are important components of
The Nitrogen Cycle is Altered by Succession
Conclusion
This study helps validate the NEON sampling design and ability
of data collected to address biologically meaningful questions.
References
1. 
2. 
3. 
4. 
2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings.
Don J. Brenner; George M. Garrity; Noel R. Krieg; James T. Staley (2005). proteobacteria: The alpha-, beta-, delta-, and epsilonproteobacteria. Springer
Science. pp. 326–327.
Shammas, N. K. (1986). Interactions of temperature, pH, and biomass on the nitrification process. Journal (Water Pollution Control Federation), 52-59.
Jain, A., Yang, X., Kheshgi, H., McGuire, A. D., Post, W., & Kicklighter, D. (2009). Nitrogen attenuation of terrestrial carbon cycle response to global
environmental factors. Global Biogeochemical Cycles, 23(4).
Contact Information: [email protected]
University of Michigan, Senior
© 2013 National Ecological Observatory Network, Inc. All rights reserved. The National Ecological Observatory Network is a project sponsored by the National Science Foundation and managed under cooperative agreement by NEON, Inc. This material is based upon work supported by the National Science Foundation under the following grants: EF-1029808, EF-1138160, EF-1150319 and DBI-0752017. Any opinions, findings, and conclusions or recommendations
expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.