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Bienvenue à Lyon!

Bienvenue à Lyon!

The lab has moved to France and joined the French National Centre for Scientific Research (CNRS) within the Laboratoire Ecologie Microbienne at the University of Lyon. This is a view of from a Ferris Wheel in Lyon's historical Bellecour

8th Labiversary at Michigan State, 2022

8th Labiversary at Michigan State, 2022

3 graduations this spring == 3 piñatas!

Happy 7th Labiversary!

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!

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!

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

Sun peaks through the miscanthus

Our lab studies how microbes may be harnessed to help bioenergy crops grow on marginal lands.

Photosynthesis!

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

"Rhizotrons" of common bean

We want to understand relationships between plants, soil, and microbes.

Centralia, PA

Centralia, PA

The landscape of Centralia - barren rock with steaming active vents adjacent to early successional vegetation.

Leaf isolates from switchgrass

Leaf isolates from switchgrass

Leaf surfaces are harsh environments. How do the microbes that live on leaves benefit plants?

EDAMAME2015

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 Biomedical Physical Sciences

MSU offers a fantastic environment for research in microbial ecology!

ArsenicResistantBacteria

ArsenicResistantBacteria

Phenotypic diversity among colonies of arsenic-resistant bacteria isolated from soil. Photo credit: Taylor Dunivin.

Arabidopsis seedlings

Arabidopsis seedlings

We want to understand how microbes communicate with each other and with their host plants using chemical signals.

Charismatic methylobacterium!

Charismatic methylobacterium!

A commensal member of the Arabidopsis phyllosphere microbiome.

Community metabolite extraction

Community metabolite extraction

In the ShadeLab, we use community metabolomics to understand microbial interactions.

Group Photo Fall 2017

Group Photo Fall 2017

Welcome to the website of Ashley Shade's research program at Université Claude Bernard Lyon 1 with the Laboratoire Ecologie Microbienne! 

#ShadeLab  #resilience

 
Microbial communities (also called microbiomes) are composed of up to tens of thousands of different types of microbial members, including bacteria, fungi, viruses, and tiny eukaryotes. These communities perform essential functions  for their ecosystems. In our research, we want to understand how environmental microbiomes respond to the changing climate. The capacity to recover quickly and fully from a large stress is called resilience, and our research aims to determine the mechanisms that support resilient systems.
 
We want to understand:
  • the relationship between microbial diversity and resilience;
  • the microbial traits and mechanisms that promote resilient communities;
  • how to predict a shift in microbiome performance, and how and when to intervene to prevent it
  • functional redundancy - when more than one microbial population can perform identically- and its importance for stable microbiome performance; and
  • how interactions among different microbes influence resilience. 
 
We know that microbiomes are generally sensitive to changes in their environment and to stress. Excitingly, many microbiomes have an immense capacity for resilience. Therefore, we hypothesize that there are ecological 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 any particular microbiome host or ecosystems. We aspire that this work will broadly advance fundamental and predictive microbiome science.
 
We have worked in many environments to understand the general aspects of microbiome resilience. We currently study environmental microbiomes from: soils, plants 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 across many environments.
keywordsmicrobial ecology and evolution, soil microbiome, plant microbiome, plant resilience, disturbance ecology, rarity, dormancy, temporal dynamics, environmental microbiology, microbial diversity, macroecology, metagenomics, metabolomics, synthetic communities
Affiliations
Laboratoire Ecologie Microbienne UMR 5557, Université Claude Bernard Lyon 1
CNRS - Institute of Ecology and the Environment
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