CAN VARIATION IN SOIL MICROBIAL COMMUNITIES HELP US UNDERSTAND INVASIVENESS

OF PLANTS?

TR Muth, Norris Muth, & Gabrielle Cannon

Why are native species often outcompeted by introduced species?

Background: Invasive species present an applied problem as well as an opportunity to address basic research questions.

introduced purple loosestrife native cattails

Acer as a Model System

Invasive Status

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invasivenon-invasive

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.

Research Goals

Hypotheses

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.

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

Learning Goals

Evolution Evolutionary history and biogeography Local adaptation (or lack thereof) OTUs and evolutionary distance (e.g.

UniFrac data)

  Systems

Positive and negative interactions between plants and soil microbial communities (e.g. mycorrhizae, pathogens, plant growth promoting bacteria, allelopathy).

V&C Core Concepts

Ability to Apply the Process of Science Study design, sample collection, DNA (RNA) purification,

barcoding and relevant preparation steps specific for intended NGS platform

Ability to Use Quantitative Reasoning Statistical analysis

Ability to Tap Into the Interdisciplinary Nature of Science Overlaps between conservation, community ecology,

microbiology, bioinformatics

Ability to Understand the Relationship Between Science and Society Intentionally introduced species and globalization Community composition and ecosystem service

V&C Core Competencies

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

DNA Sequence Requirements

Earth Microbiome Project, J. Gilbert Laboratory

Ability to support QIIME and R. Need for cluster access will depend on the size of the data sets.

Computational Requirements

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

Assessment

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)

Lecture Topics

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?

Discussion Topics

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.

Unit 1: Identify systems and/or study sites Unit 2a: Collect and process samples Unit 2b. Troubleshooting sample processing  -sequence samples or send samples for sequencing-

Unit 3: Revisit background context – the relevance of biogeography, community interactions, & evolution

Unit 4: Computation and analysis

Time Line

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References