Transcript CAN variation in SOIL microbial communities help us understand

CAN VARIATION IN SOIL
MICROBIAL COMMUNITIES
HELP US UNDERSTAND
INVASIVENESS OF PLANTS?
TR Muth, Norris Muth, & Gabrielle Cannon
Background: Invasive species present an applied
problem as well as an opportunity to address basic
research questions.
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Why are native species often outcompeted by
introduced species?
introduced purple loosestrife
native cattails
Acer as a Model System
Invasive Status
alien
native
Introduction Status
non-invasive
invasive
Research Goals
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Characterize the differences in root microbial
communities between introduced invasive species and
native species (congeners).
Investigate possible role of root microbial community
members in facilitating growth of introduced invasive
species or constraining the growth of native species.
In turn, investigate the role of introduced invasive
species on soil microbial communities.
Hypotheses
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To the extent that invasive plants (introduced or
native) are generalists, we expect to see them
associated with common widespread fungal taxa,
while rare fungal taxa are more often associated
with non-invasives.
Furthermore, we expect greater diversity of soil
fungi to be associated with native species, while
introduced species should have fewer co-adapted
associates.
Learning Goals
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After participation in this module students should be
able to –
 determine native and introduced ranges of a
species
 develop or critically evaluate sample collection and
sample processing protocols relevant to
metagenomic study
 use QIIME to process and analyze metagenomic
data sets
V&C Core Concepts
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Evolution
 Evolutionary
history and biogeography
 Local adaptation (or lack thereof)
 OTUs and evolutionary distance (e.g. UniFrac data)
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Systems
 Positive
and negative interactions between plants and
soil microbial communities (e.g. mycorrhizae, pathogens,
plant growth promoting bacteria, allelopathy).
V&C Core Competencies
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Ability to Apply the Process of Science
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Ability to Use Quantitative Reasoning
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Statistical analysis
Ability to Tap Into the Interdisciplinary Nature of Science
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Study design, sample collection, DNA (RNA) purification, barcoding
and relevant preparation steps specific for intended NGS platform
Overlaps between conservation, community ecology, microbiology,
bioinformatics
Ability to Understand the Relationship Between Science
and Society
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Intentionally introduced species and globalization
Community composition and ecosystem service
DNA Sequence Requirements
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Illumina MiSeq sequencing of the 18S rRNA ITS
region
Could be expanded to bacteria through 16S rRNA
gene sequencing
Could be expanded to whole genome shot-gun
sequencing and/or RNA-Seq
Earth Microbiome Project, J. Gilbert Laboratory
Computational Requirements

Ability to support QIIME and R. Need for cluster
access will depend on the size of the data sets.
Assessment
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Pre and post tests to include coverage of:
 content
 plant-soil
microbial interactions
 local adaptation
 biogeography and invasive species
 metagenomic techniques and applications
 attitudes/awareness
 scientific inquiry
 centrality of evolution to biology / utility of evolution as
applied science
 invasive species
Lecture Topics
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Plant-soil Communities – specifically, plant-plant (competition,
inhibition) and plant-soil microbial interactions (mutualisms,
pathogenicity, etc.)
Community diversity
Adaptation and co-evolution (as relating to species
interactions)
Biogeography and dispersal (patterns, mechanisms,
consequences)
Principles of metagenomics (sequencing and sequence
variation, taxa and target regions, OTUs, community analysis)
Discussion Topics
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To what extent do plant communities determine the niches
of soil microbial communities, or vice versa?
If native species are adapted to their local conditions,
why do introduced invasive species out compete them?
If dispersal of organisms is a normal process, can we
meaningfully distinguish native and introduced species?
Time Line
Variable depending on whether only computational work will be performed
(on pre-existing data) or whether both sample collection/processing and
computational work will be included in a more comprehensive manner.
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Unit 1: Identify systems and/or study sites
Unit 2a: Collect and process samples
Unit 2b. Troubleshooting sample processing
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-sequence samples or send samples for sequencing-
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Unit 3: Revisit background context – the relevance of biogeography,
community interactions, & evolution
Unit 4: Computation and analysis
References
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