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![Page 1: Dyhrman Lecture partBv2 - Home - Evolution and Genomicsevomics.org/wp-content/uploads/2015/06/Dyhrman-Lecture-part-2.pdf · Other terpenoid biosynthesis Replication system Sterol](https://reader030.fdocuments.us/reader030/viewer/2022041206/5d5b08f488c99336108bcac4/html5/thumbnails/1.jpg)
• From genome to biome: Tracking themetabolism and microbiome of a keystoneN2 fixer
• Co-‐exis>ng in a sea of compe>>on:Leveraging transcriptome data to iden>fythe physiological ecology of phytoplanktonfrom key groups
Vigne&es
Genome -‐ enabled
Transcriptome -‐ enabled
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Fe ZnB12
NO3-‐
PO4-‐
SiO42-‐
Light
Preda7on
Nutrients
Complex community dynamics driven in part by resources
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Culture and field based approaches to physiological ecology
Genome and transcriptome-enabled advances allowing to querycells in their environment in a species specific way
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Key themes
• Our focus is on groups that arguably serve a“keystone” role in the marine ecosystem
• Biogeochemical drivers of physiology:– What are the mechanistic underpinnings of resource
utilization and how does resource utilization vary overtime?
• Eco-evolutionary traits:– Are there functional group traits that drive the structure
and function of the NPSG?
• Metabolic plasticity and diversity:– How do diversity and metabolism influence the
physiogical ecology of a keystone group?
Hap
toph
ytes
Dia
tom
sD
inof
lage
llate
s
Harriet Alexander
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Physiological ecology -‐ a tale of two diatoms in Narraganse&Bay
• Do closely related diatoms have the same expressed metaboliccapacity?
• Is this metabolic profile consistent over >me?• Are the resource responses the same between species, or is there
evidence of resource par>>oning of niche space?
Skeletonema T. rotula
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Collect samplesfrom NB Bay Isolate mRNA AAAAAA
AAAAAAAAAAAA
AAAAAA
Submit samplesto sequencingcenter
Sequence usingRNAseq and mapreads to genomes
Sampling and pipeline
Stringent mapping
Target 60 million100 bp paired-‐end reads
Removed reads withambiguous mapping
Thalassiosira rotulaSkeletonema costatumand … rest of MMETSP~400 transcriptomes
48hr incuba>onat day S3
>5µm
MMETSP = Marine Microbial Eukaryo>c Transcriptome Project
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Reference Database
Read Mapping andCoun7ng
Quality Control
Metatranscriptome Data Pipeline -‐ the gory details ….
Data Crea7on
Extract RNA
Sequence RNA:(Illumina 60M100bp PE)
Each read file = 15-‐25GbEach sample = 30-‐50Gb
Trimmoma7c:
Remove lowquality reads
Bow7e2:Map sequences to
referencetranscriptomes
Select referencetranscriptomes
CD-‐HIT-‐EST:Cluster at
98% iden>tyby species
Bow7e2-‐build:Create
database formapping
Re-‐annotate?
Renamecon>gs andconcatenate
Custom Script:Create ar>ficial
GFF file
Samtools:Sort and convertmapped file to
accessible format
HT-‐Seq/RSEM:Count reads by
gene
RawSequnceFile.fastq
TrimmedSequnces.fastq
RawCounts.tab
FastQC:Assess library
quality
MappedSequences.bam
MappedGenesSorted.sam
Ref.gff
Ref.fa
8
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Collect samplesfrom NB Bay Isolate mRNA AAAAAA
AAAAAAAAAAAA
AAAAAA
Submit samplesto sequencingcenter
Sequence usingRNAseq and mapreads to genomes
Sampling and pipeline
Stringent mapping
Target 60 million100 bp paired-‐end reads
Removed reads withambiguous mapping
Thalassiosira rotulaSkeletonema costatumand … rest of MMETSP~400 transcriptomes
48hr incuba>onat day S3
>5µm
Local isolates provide the most robust read mapping (15Xincrease for local isolate rela>ve to species in database) -‐ liclemapping (<<1%) to diatoms not present in this system
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Taxonomic distribu7on of reads
S 1- 5
Skeletonema
S 1- 5
Alexander et al. 2015 PNAS
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C entral carbohydrate metabolismRibosom e
Carbon f ixationOther carbohydrate metabolism
Spliceosom eATP synthesis
Aminoacy l tR NAPurine metabolism
RNA processingBranched-chain amino ac id metabolism
Cysteine and m ethionine metabolismC ofactor and vitamin biosynthesis
Methane metabolismMetabolic capacity
Proteasom eUbiquitin system
Protein processingPhotosynthesis
Lysine metabolismRNA polymerase
Pyrimidine metabolismFatty ac id metabolism
Lipid metabolismAromatic amino ac id metabolismArginine and proline metabolism
Nitrogen metabolismSulfur metabolism
Terpenoid backbone biosynthesisSerine and threonine metabolism
Repair systemNucleotide sugar
Glycan metabolismPolyam ine biosynthesis
Glycosaminoglycan metabolismOther terpenoid biosynthesis
Replicat ion systemSterol biosynthesis
Histidine metabolismABC-2 type and other transport systems
Bacterial sec ret ion systemDNA polymerase
Sugar metabolismPhosphate and amino acid transport systemPheny lpropanoid and flavonoid biosynthesis
Saccharide and polyol t ransport systemAlkaloid and other secondary m etabolite biosynthesis
Other amino ac id metabolismTw o-component regulatory system
Mineral and organic ion transport systemMetallic cat ion and vitam in B12 transport system 1 0-5
1 0-4
1 0-3
1 0-2
1 0-1
S 1 S2 S3 S4 S5 S1 S2 S3 S4 S5S. costatum T. ro tula
Branched-chain amino ac id metabolism
Pe
rce
nt o
f KE
GG
An
no
tated
Re
ad
sKEGG Module
Expressed metabolic capacity
Quan>ta>ve Metabolic Fingerprint(QMF)
Plas>c responses over >me
Unique responses between diatom genera
Skeletonema
Alexander et al. 2015 PNAS
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QMF highlights the metabolic traits and tradeoffs
Skeletonema
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Variability in expressed metabolic capacity for N and P
Skeletonema
Alexander et al. 2015 PNAS
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Transcripts are choreographed with proteins and ac7vi7es inthe model diatom Thalassiosira pseudonana
Dyhrman et al. 2012 PLoS ONE
+P -P
GDP
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Transcripts are choreographed with proteins and ac7vi7es inthe model diatom Thalassiosira pseudonana
Dyhrman et al. 2012 PLoS ONE
+P -P
NPT
Inc uptake
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Variability in expressed metabolic capacity for N and P
Skeletonema
Alexander et al. 2015 PNAS
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Iden7fying the resource responsive gene set
• Resource responsive? Sta>s>callyiden>fy resource responsive set (-‐Nv. +N; -‐P v. +P)
• Stable? Sta>s>cally iden>fy stablereference genes (no change overincuba>ons)
• Normalize to reference genes(SGNC)
+P -PVS -N+N VSP-‐responsive
genesN-‐responsive
genes
• Incuba>ons performed with shiled N:P ra>o to provide context for insitu signals
Alexander et al. 2012 Front. Micro.
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Resource responsive genes iden7fied in situ
• Resource responsive sets are dis>nct fromeach other and enriched in pathways of Nand P metabolism (e.g. urease,phosphatase, phosphate transport etc.)
• Can assign regula>on pacerns to novelgene families
• But how do we compare signals betweenspecies? Alexander et al. 2015 PNAS
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Propor7onalize the resource responsive gene set
(SGNC-‐P) – (SGNC+P )
(SGNCfield) – (SGNC+P)STDP =
(SGNC-‐N) – (SGNC+N)
(SGNCfield) – (SGNC+N)STDN =
Standardized transcrip7onaldifferen7a7on scores
STDP ≈ 1 -‐PSTDP ≈ 0 +P
STDN ≈ 1 -‐NSTDN ≈ 0 +N
Alexander et al. 2015 PNAS
+P -PVS -N+N VSP-‐responsive
genesN-‐responsive
genes
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STDP
High N or Low P
Low N or High P
-‐P
+P
-‐N+N
STDP
Visualizing resource responsive signals in the field
STDN
Alexander et al. 2015 PNAS
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STDP
S2High N or Low P
Low N or High P
-‐P
+P
-‐N+N
STDP
T. rotulaSkeletonema
Up in -‐P
Up in -‐N
Visualizing resource responsive signals in the field
STDN
Alexander et al. 2015 PNAS
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Species variability in response to the same environment
• Finely tuned species-‐specific varia>on -‐ each response (quadrant) issignificantly different from the others
• Responses are orthogonal between species in the same resourceenvironment
Alexander et al. 2015 PNAS
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Summary - Biogeochemical drivers of physiology
• New approaches for the normaliza>on andcomparison of metatranscriptome data.
• Diatom metabolism is highly variable in thisestuarine environment
• Uniquely expressed metabolic capacityunderpins Skeletonema bloom … and trade offsin N and P metabolism that contribute to thedominance of one diatom over another
• Pacerns in resource par>>oning may reflectsegrega>on of the realized niche space andexplain why so many diatom species can co-‐occur
Phosphate transport
Nitrate reduc7on
What are the mechanistic underpinnings of resource utilization andhow does resource utilization vary over time?
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Key themes
• Our focus is on groups that arguably serve a“keystone” role in the marine ecosystem
• Biogeochemical drivers of physiology:– What are the mechanistic underpinnings of resource
utilization and how does resource utilization vary overtime?
• Eco-evolutionary traits:– Are there functional group traits that drive the structure
and function of the NPSG?
• Metabolic plasticity and diversity:– How do diversity and metabolism influence the
physiogical ecology of a keystone group?
Hap
toph
ytes
Dia
tom
sD
inof
lage
llate
s
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The significance of the NPSG
Image credits: SeaWIFS Global Chlorophyll
North PacificSubtropicalGyre
Sta7on ALOHA
(Karl and Church, Nature Rev. Microbiol., 2014)
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The keystone microbiome
Nutrient input,or other forcings
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Hawaii Ocean Experiment: Dynamics of Light and Nutrients
(HOE-DYLAN)
Wilson et al. 2015 GBC
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Harriet Alexander
Sampling a bloom
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Deep water addi7on led to simulated “bloom”
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Collect samplesfrom St. ALOHA Isolate mRNA AAAAAA
AAAAAAAAAAAA
AAAAAA
Submit samplesto sequencingcenter
Sequence usingRNAseq and mapreads to genomes
Sampling and pipeline
Stringent mapping
Target 60 million100 bp paired-‐end reads
Removed reads withambiguous mapping
MMETSP ~400transcriptomes
6 day incuba>ons
>5µm
MMETSP = Marine Microbial Eukaryo>c Transcriptome Project
![Page 31: Dyhrman Lecture partBv2 - Home - Evolution and Genomicsevomics.org/wp-content/uploads/2015/06/Dyhrman-Lecture-part-2.pdf · Other terpenoid biosynthesis Replication system Sterol](https://reader030.fdocuments.us/reader030/viewer/2022041206/5d5b08f488c99336108bcac4/html5/thumbnails/31.jpg)
Marine Microbial Eukaryote Transcriptome Sequencing Project
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Keeling et al. 2014 PLoS Biol.
Greatly expanded reference sequences in the tree of life
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Within lineage diversity also greatly expanded
Keeling et al. 2014 PLoS Biol.
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MMETSP improves read iden7fica7on
Sequence read iden>fica>on is substan>ally improved over usingphytoplankton genomes which do not capture the same diversity.
Read mapping against genomes v. MMETSP at St. ALHOA
Alexander et al. 2015b PNAS
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Taxonomic distribu7on of reads
Distribu>ons is highly stable, much more so than what was observed incoastal system.
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Increase in diatoms during simulated blooms
Read iden>fica>on is robust, most are dinoflagellates, but diatomsincrease in simulated blooms (+DSW)
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DIA HAP DIN
ENERGYMETABOLISM
CARBOHYDRATEAND LIPID
METABOLISM
NUCLEOTIDE ANDAMINO ACIDMETABOLISM
GENETICINFORMATIONPROCESSING
METABOLISM
Alexander et al. 2015b PNAS
ENVIRONMENTALINFORMATIONPROCESSING
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Quan7ta7ve metabolic fingerprint
Species are dis>nct from each other with 95% confidence, and all butdinoflagellates significantly shil in the simulated blooms
For each gene determineSignificance Post-‐p > 0.95 for 2-‐fold change
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Gene shies in diatoms
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Gene shies in diatoms
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Transcrip7onal response during simulated blooms
Alexander et al. 2015b PNAS
Functional groups have distinct and reproducible transcriptional responseduring blooms driven by nutrient input
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42
Variable TranscriptAlloca>on Ra>o (VTAR)
Variable transcript alloca7on underpins traits
Haptophytes: “the survivalists”; VTAR<1Diatoms: “the scavengers”; VTAR>1
• Modeling transcript alloca>onfollowing nutrient addi>onhighlights differences in diatomand haptophyte traits
• Diatoms are more efficient thanhaptophytes
Alexander et al. 2015b PNAS
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Transcrip7onal responses underscore func7onal group traits
Dinoflagellates
Alterna>ve trophicmodes?
FEW significant shils
BROAD transcript decreasesTARGETED transcript increase
“the scavengers” r-‐selected
“the survivalists” K-‐selected
MUTED increase and decreases
Diatoms
Haptophytes
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Summary - Eco-evolutionary traits
• The becer the reference database(MMETSP) the becer resolu>on
• Phytoplankton groups appear to be limitedby resource availability in the NPSG.
• Dinoflagellates have licle transcrip>onalresponse to nutrient input.
• Diatom are par>cularly responsive(VTAR>1) to nutrient input which likelyunderpins their dominance in blooms
Are there functional group traits that drive the structure andfunction of the NPSG?
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Key themes
• Our focus is on groups that arguably serve a“keystone” role in the marine ecosystem
• Biogeochemical drivers of physiology:– What are the mechanistic underpinnings of resource
utilization and how does resource utilization vary overtime?
• Eco-evolutionary traits:– Are there functional group traits that drive the structure
and function of the NPSG?
• Metabolic plasticity and diversity:– How do diversity and metabolism influence the
physiological ecology of a keystone group?
Hap
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ytes
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Diving beyond the func7onal group…
Tracking strain specific responses in the calcifyinghaptophyte, Emiliania huxleyi (Ehux)
Image: Jeremy Young
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asexual division
2NDiploid
Calcifying
asexual division
1NHaploid
MEIOSIS(diploid divides to
haploid)
SYNGAMY(two haploids fuse
to diploid)
Naked
E. huxleyi life cycle
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Emiliania huxleyi: a cosmopolitan, globally significant species
Image: NASA Earth Observatory
• Calcifica>on -‐ cri>cal role inglobal carbon cycle andstrongly linked to climatedriven ocean acidifica>on
• Source of paleoproxies forclimate reconstruc>ons
• Form dense blooms, driverslargely unknown
• First marine phytoplankton tohave mul>ple strainssequenced, iden>fying pangenome
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10,000 cells per ml> 100,000 km2
Figure from Read et al., 2013
Emiliania huxleyi has many diverse isolates
Cultured strains are highly diverse -‐ isolated from a broadtemperature range and displaying considerable physiological diversity
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E. huxleyi has a pan genome, with core and variable genecontent
Key func>onal genes are variably distributed across cultured isolates.
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Hawaii Ocean Experiment: Dynamics of Light and Nutrients
(HOE-DYLAN)
Wilson et al. 2015 GBC
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C
Control
+NDSW
Deep seawater amendment
-‐N +P-‐P
Treatments with added N
Responses to shies in resource ra7os
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Collect samplesfrom St. ALOHA Isolate mRNA AAAAAA
AAAAAAAAAAAA
AAAAAA
Submit samplesto sequencingcenter
Sequence usingRNAseq and mapreads to genomes
Sampling and pipeline
Stringent mapping
Target 60 million100 bp paired-‐end reads
Removed reads withambiguous mapping
MMETSP Ehux straintranscriptomes
6 day incuba>ons
>5µm
MMETSP = Marine Microbial Eukaryo>c Transcriptome Project
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Summary -‐ Metabolic plas7city and diversity
• Metatranscriptome data can be parsed atthe strain level with appropriate referencedata.
• Apparent abundance of Ehux strains andtheir physiology is driven by nitrogenaddi>on
• Everything is perhaps everywhere and theenvironment selects for what is dominant
How do diversity and metabolism influence the physiogical ecologyof a keystone group?
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Summary
• Biogeochemical drivers of physiology:– Plasticity in diatom physiology may allow for co-
occurrence of diverse species.
• Eco-evolutionary traits:– Diatoms appear to be more efficient in turning over
their transcriptome than haptophytes which likelyunderpins their success in response to nutrient pulsesin the NPSG.
• Metabolic plasticity and diversity:– E. huxleyi strains vary in the field in response to N, but
harbor conserved responses to nutrient pulses in theNPSG.
• New resources and ways of parsingmetatranscriptome data are leading to newinsights!
Hap
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Dia
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• Dyhrman Lab: Dr. Rachel Wisneiwski Jakuba, Dr. Elizabeth Orchard, Dr. LouieWurch, Abigail Heithoff, Harriet Alexander, Kyle Frischkorn, Dr. Alena Sevucu, Dr.Julia Diaz, Dr. Monica Rouco Molina, Hannah Joy-Warren, Sheean Haley andmany undergraduate interns.
• Collaborators: Ben Van Mooy, C-MORE partnership, Mike Lomas and the BATSProgram, Jim Ammerman and the ATP3 Program, Eric Webb, Claudia Benitez-Nelson, Ellery Ingall, Dan Repeta, Dennis McGillicuddy, John Waterbury, CabellDavis, Mak Saito, Bethany Jenkins, Tatiana Rynearson, C-MORE investigators
Acknowledgements
• C-‐MORE• Simons Founda>on• NSF• EPA• NOAA• DOE, JGI