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Metabolic
dynamics of
Colorado Plateau
Biological Soil
Crusts
Trent Northen
March 13th 2012, Moab UT
Berkeley Lab
ms.lbl.gov
Effect of changing rainfall on the crust
• Models predict changes in precipitation amounts and seasonality
• Complement the descriptive studies with detailed mechanistic studies
(systems approaches) on the dynamics of wetting to help predict crust
responses to changing rainfall patterns
Goal: Define the functional dynamics in natural
communities in response to a single-wetting event.
a
b
d
0 min
Green Butte, Colorado Plateau
15min
e
30 min after wetting
Belnap J., 2006. Hydro. Process.
a: USGS Canyonlands Research Station
b: Belnap etal
c: Zhang, Y. 2005. Chin. Sci. Bulletin.
d: Garcia-Pichel AEM 2001
e: Gerritsen 2002 BIODIDAC
Pulse-Activity Event and Biological Soil Crust
• Life in the edge of habitability
• Long periods without water
• Suddenly:
Green Butte sampling location Moab, Utah late
June 2011
Microcoleus vaginatus
Microcoleus vaginatus
Belnap J., 2006, Hydrol. Process.
Image. Ferran Garcia-Pic
Microcoleus vaginatus PCC 9802 Genome
Annotation
• Hand-curated 385 genes out
of 5264 predicted by IMG/ER.
Pathway Overview
• Validated the putative functional
assignment of 201 genes including
168 enzymatic functions (via
homology and active site checks).
•Out of these 201 genes,
135 matched their IMG functional
prediction, 9 had different functional
assignments, and 15 had unique
functional assignments.
Generated with KEGG Atlas
Microcoleus Vaginatus PCC 9802
Genome Annotation & Modeling
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Pathways Predicted
Pathways NOT Predicted
TCA Cycle
Pentose Phosphate Cycle
Glycolysis
Photosynthesis-Light Reactions
Photosynthesis- Antennae Proteins
Peptidoglycan Biosynthesis
Glycogen Biosynthesis
20 Amino Acids Biosynthesis
Homolactic Fermentation
Nitrate Assimilation
Ammonium Assimilation
Sulfate Reduction
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Mixed Acid Fermentation
Heterolactic Fermentation
Nitrogen Fixation
Syctonemin Biosynthesis
Experimental design
We simulated rain and followed the behavior of the
crust for 6 days (day and night)
Wet-up
Gas phase and pore water metabolites dynamics
Microarray Expression Analysis
DNAase
treat
whole
transcriptome
amplifica on
RNA from crust
amplified cDNA
Label with Cy3
array represents 6130
genes from M.vaginatus
PCC9802 and FGP-2
data
analysis
RMA
normaliza on
hybridize to
Nimblegen
expression array
k-means
clustering
Correlation plot
Early phase clusters – preliminary sorting
Cluster 1 – peaks at 3 min – Includes only a handful
of genes with known functions – signaling, TA
loci?, methylases, DNA repair, ATPases
Cluster 2 – increases after 3 min upto 9 h –
Includes nitrate and sugar transport genes,
cyanophycinase, RNA binding proteins, fatty acid
metabolism, phycobilisomes, CCM genes, several
proteases, cell division FtsZ, glycogen synthesis, aa
synthesis
Cluster 3 – increases after 15 min up to 9hr.
Includes chlorophyll synth, ATP synthase,
respiration, electron transport, nitrogen
metabolism, pili, ribosomal genes, sulfate
transport
Cluster 4 – peaks at 15 min. chaperones and
oxidative stress, DNA repair, signaling and
regulation
Cluster 5 – peaks at 0 and decreases –– oxidative
stress (includes orange carotenoid, catalase,
chaperones), phycobilisome degradation prtn,
chlorophyll binding prtn, trehalose synthase,
ppGPp synthetase, PHA synthase, cyanophycinase,
signaling and regulation
Diel genes – core clusters
Cluster 1: peaks at dusk – no
photosynthesis genes. Ribosomal
genes, respiration (cytochrome
oxidases)
Cluster 2 - peaks at day – Most PSII
genes, most phycobilisome genes,
GroES/EL chaperones and Clp
proteases, oxidative
phosphorylation
Cluster 3- peaks at night – PSI and
some PSII, Carboxysome assembly,
Rubisco genes
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2
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Dry genes core clusters
• Cluster 1 – decreases from
start of dry; includes
translation and cell division
genes
• Cluster 2 – increases from
start of dry; includes
oxidative stress,
glycosyltransferases
• Cluster 3 – decreases 1 hr
after start of drying; includes
oxidative phosphorylation,
chlorophyll synthesis
• Cluster 4 – increases 3 hrs
after drying
• Cluster 5 – peaks at 3 hrs
from start of dry; includes
signaling, sucrose synthase
Dynamic responses to pulsed-activity event
Relative activity
Heterotroph 2
Heterotroph 1
Cyanobacteria
Time
T0: Meta-genomics
Meta-proteomic analysis
To define crust composition
Reconstructing
the microbial
food web
Photosynthetic cyanobacteria
provide fixed C and N to an
otherwise nutrient poor
environment.
A complex network of microbial
interactions results in C
sequestration or mineralization.
Acknowledgem
ents
LBNL
Trent Northen
Benjamin Bowen
Aimee Johnson
Kriti Sondhi
Nicholas Jose
David Soendjojo
Eoin Brodie
Julian Fortney
Nicholas Bouskill
Rohit Salve
JBEI
Aindrila Mukhopadhyay
Lara Rajeev
Eric Luning
Chris Petzold
JGI
Cheryl Kerfeld
Seth Axen
ASU/LBNL
Ferran Garcia-Pichel
Ruth Potrafka
LBNL LDRD Support
Thanks for your attention
Dry-down