engineering soil microbes as environmental biosensors · 2016-11-13 · engineering soil microbes...
TRANSCRIPT
Engineering soil microbes as environmental biosensors
Synthetic biology can be used to develop tools needed to study the environmental microbiome and how it responds to biogeochemical change
Lin Boynton2,3, Hsiao-Ying Cheng1, Ilenne Del Valle3, Joff Silberg1,3, Caroline Masiello2,3
1Bioengineering, 2Earth Science and Chemistry, 3BioScience, Rice University, Houston, TX
GC-MS
The biogeochemical cycles are currently undergoing major change
Interdisciplinary tools are needed to characterize biogeochemical interactions
After Chorover et al, Catalina-Jemez CZO
The
critical
zone
Earth science is successful with top down methods
Google images
• Environmental Fluxes• Climate models• Paleobiology
Soil science
Measures NET greenhouse gases (GHG)
Net GHG
Metagenomics has begun to address environmental microbiology questions
All microbe DNA
provides the genetic information of all microbes in the sample
Metagenomics
Soil science
Measures NET greenhouse gases (GHG)
methanogens methanotrophs
denitrifiers nitrifiers nitrogen fixers
autotrophs heterotrophs
lithotrophs
Net GHG
Metagenomics has begun to address environmental microbiology questions
methanogens methanotrophs
denitrifiers nitrifiers nitrogen fixers
autotrophs heterotrophs
lithotrophs
Metagenomics
offers a SNAPSHOT of gene activity which gives an idea of function
Transcriptomics
ALL microbe dNA
Soil science
Net GHG
Metagenomics has begun to address environmental microbiology questions
RNA & PROTEINS
Visual reporting methods not useful for nontransparent environmental samples
Fluorescence
bioluminescence
Sadikot et al NCBI, 2005usgs.gov
Soil samples
water samples
chemistryGC-MS Trace Gas
Microbial biosensors are a solution to biogeochemical challenges
GC-MS
Microbial biosensors use gas reporting
Environmental
stimulus
Trace Gas
Production
Real time
measurement
The Design
POCThe
MicrobeIt Works the idea
The Future
POC in E. coli shows good signal in environmentally relevant conditions
The Design
POCThe
MicrobeIt Works the idea
The Future
Volatile Gas Production by Methyl Halide Transferase: An In Situ Reporter Of Microbial Gene Expression In SoilHY Cheng, CA Masiello, GN Bennett, JJ Silberg - Environmental Science & Technology, 2016
• P. stutzeri is a gram negative, denitrifying bacterium
• Important in the N cycle
NO3- NO2
- NO N2O↑ N2
• Quick and easy to culture and manipulate
• Common in soil environments
Pseudomonas stutzeri is ideal for engineering a biogeochemically important biosensor
The Design
POCThe
MicrobeIt Works the idea
The Future
Good signal at environmentally relevant concentrations of substrate in P. stutzeri
0
100
200
300
400
500
600
700
800
900
1mM 25mM 50mM 100mM 200 mM 400mM
WT
MHT
The Design
POCThe
MicrobeIt Works the idea
The Future
Substrate concentration (mM)
Ga
s s
ign
al
(c
ou
nt
s)
Microbial biosensors are a way to trace biogeochemical processes in the N cycle
The Design
POCThe
MicrobeIt Works the idea
The Future
The chemistry of the N cycle is well studied; biology beginning to be better understood
The Design
POCThe
MicrobeIt Works the idea
The Future
We are targeting a comprehensive microbial tool kit for the N cycle
Rhizobium leguminosarum
Azotobactervinelandii
Pseudomonas stutzeri
Nitrosomonaseuropaea
The Design
POCThe
MicrobeIt Works the idea
The Future
System is working – possibilities for a nitrogen specialist microbial biosensor
The Design
POCThe
MicrobeIt Works the idea
The Future
Future directions:
• Broad host expression
• C, N, P nutrient limitation/ heterogeneity
• Critical zone field experiments
Thank you
Silberg lab:
Shelly Cheng
Ilenne Del Valle
Dongkuk Huh
Shirley Liu
Josh Atkinson
Emily Thomas
Ian Campbell
Masiello Lab:
Xiaodong Gao
Valérie Huguet
Zuolin Liu
Lacey Pyle
Loredana Suciu