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shade lab

understanding the rules of microbiome resilience

Happy 7th Labiversary! After missing our 6th Labiversary party due to the COVID19 pandemic, the ShadeLab celebrated its 7th Labiversary in July 2021.	We've grown! We've moved! Abby and Keara, be-masked and socially distant in our new lab in rm 6144/6150 Biomedical Physical Sciences Building!	Happy 5th Labiversary! Dufour and Shade lab members and their families celebrated our 5th Labiversary at Michigan State in July 2019
Sun peaks through the miscanthus Our lab studies how microbes may be harnessed to help bioenergy crops grow on marginal lands.	Photosynthesis! False-colored image of Arabidopsis plants taken in MSU's Center for Advanced Algal and Plant Phenotyping. Axenic plants were inoculated with different combinations of core members of the phyllosphere community.	"Rhizotrons" of common bean We want to understand relationships between plants, soil, and microbes.
Centralia, PA The landscape of Centralia - barren rock with steaming active vents adjacent to early successional vegetation.	Leaf isolates from switchgrass Leaf surfaces are harsh environments. How do the microbes that live on leaves benefit plants?	EDAMAME2015 The Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology course at Kellogg Biological Station in 2015, posing as a double helix. Photo credit: Tom Rayner, @tomonlocation
MSU Biomedical Physical Sciences MSU offers a fantastic environment for research in microbial ecology!	ArsenicResistantBacteria Phenotypic diversity among colonies of arsenic-resistant bacteria isolated from soil. Photo credit: Taylor Dunivin.	Arabidopsis seedlings We want to understand how microbes communicate with each other and with their host plants using chemical signals.
Charismatic methylobacterium! A commensal member of the Arabidopsis phyllosphere microbiome.	Community metabolite extraction In the ShadeLab, we use community metabolomics to understand microbial interactions.	Group Photo Fall 2017

Welcome to the website of Ashley Shade's research team at Michigan State University!

#ShadeLab #SpartansWill

Microbial communities (also called microbiomes) are composed of up to tens of thousands of different types of microbial members. These communities perform functions that are absolutely essential for their ecosystems, from nutrient cycling in the environment, to priming the immune system in a plant or animal host. Many of these functions are supported by the collective community, which is why it is important to consider the microbiome as a system with many interacting parts.

In our research, we investigate the ecology and evolution of microbiomes. In particular, we want to understand how microbial communities respond to stress so that we can manage them to quickly recover. The capacity to recover quickly and fully from a large stress is called resilience. Understanding the rules of microbiome resilience will help to support healthy outcomes for hosts and environments by stabilizing the essential functions that microbial communities perform.

We want to understand:

how microbial diversity can support resilience;
the microbial traits and mechanisms that promote resilient communities;
how to predict a fundamental shift in microbiome performance, and to intervene in advance to prevent the shift
the importance of functional redundancy - when more than one microbial population can perform identically- for stable microbiome performance; and
how interactions among microbiome members influence resilience.

It is well-documented that microbiomes are generally sensitive to changes in their environment and other stresses. Excitingly, many microbiomes have an immense capacity for resilience. Therefore, we hypothesize that there are general rules of microbiome resilience that can be usefully applied across different environments. Our research is grounded in ecological framework and focused on building transferable theory, approaches, and knowledge of mechanisms that transcend microbiome hosts and ecosystems. We aspire that our work will advance fundamental and predictive microbiome science broadly.

Because we want to understand rules of microbiome resilience, we tend to work in multiple environments to determine generality. We currently study microbiomes from: plant roots, leaves, and seeds; soils impacted by a long-term and severe disturbance (the Centralia, PA coal seam fire); and synthetic communities that we create in the lab. We have also used data mining and meta-analyses to investigate broad patterns of microbial diversity in many environments, including human guts, lakes, waste water treatment, and oceans. We are happy to collaborate to think about resilience in other habitats as well.

keywords: microbial ecology and evolution, soil microbiome, plant microbiome, plant resilience, disturbance ecology, rarity, dormancy, temporal dynamics, environmental microbiology, microbial diversity, macroecology, metagenomics, metabolomics, synthetic communities