Transcript: New from BookNet Canada for 2024: BNC CataList - Tech Forum 2024
Metzger MS defense
1. Characterizing the effects of ocean acidification in larval
and juvenile Manila clam, Ruditapes philippinarum, using
a transcriptomic approach
David Metzger
University of Washington
School of Aquatic and Fishery Sciences
Committee:
Dr. Steven Roberts
Dr. Carolyn Friedman
Dr. Linda Rhodes
2. Outline
• Introduction and Background
• Ocean acidification
• Manila clam Ruditapes philippinarum
• Question 1:
How does elevated pCO2 affect larval Manila clam physiology?
• Question 2:
Does elevated pCO2 affect the susceptibility of juvenile clams to
other environmental stressors?
• Conclusions and future directions
4. Ocean Acidification
-
CO2 + H2O H2CO3 HCO3 + H+
-
CaCO3 Ca2+ + CO32- + H+ HCO3
CO2 pH Calcium Carbonate
Photo: David Mack
5. Ocean Acidification
• Calcium carbonate molecules are less available
• Calcification become a more energetically demanding process
CO2 pH Calcium Carbonate
Photo: David Mack
18. Manila Clam Habitat
• Intertidal and coastal environments
Hypoxia Salinity
Temperature Disease
19. Manila Clam Habitat
Hypothesis:
– Ocean acidification will negatively impact manila clams.
Why?
– Calcification, growth, and maintaining ion homeostasis will
become more energetically demanding.
– Less resources to cope with additional stressors of inhabiting
intertidal communities
26. Reference Assembly
Manila clam transcriptome database
http://compgen.bio.unipd.it/ruphibase/
(Milan et al., 2011)
What is RuphiBase?
• 32,606 contiguous sequences from 454 Roche pyrosequencing
• Average length 546bps
• 5,656 Sanger expressed sequence tags
• 51 mRNA sequences from NCBI
27. Reference Assembly
Manila clam transcriptome database
http://compgen.bio.unipd.it/ruphibase/
(Milan et al., 2011)
Sequence “X”
Map reads to
reference sequences
Total number of reads from elevated and 243,416,187
ambient libraries combined
Total number of contigs 27,390
28. Reference Assembly
Manila clam transcriptome database
http://compgen.bio.unipd.it/ruphibase/
(Milan et al., 2011)
Sequence “X”
Map reads to
reference sequences
Characterize by gene ontology
29. Reference Assembly cell cycle and
cell adhesion cell organization
proliferation
and biogenesis
cell-cell
signaling
death
transport
developmental
processes
DNA
metabolism
protein
metabolism
stress response
signal RNA
transduction metabolism
41. Development and Growth
20000
Shell Area (μm2)
18000
16000
14000
12000
10000
8000
1 4 7 11 14
Sampling Day
42. Candidate Gene Identification
Gene Name Ruphibase ID Fold Change Gene Function
Perlucin 6 ruditapes_lrc29501 133 Calcification
Calmodulin ruditapes_c670 4.4 Calcium binding
Cathepsin L ruditapes_c11131 3 Protein Translation
Elongation factor 2 ruditapes2_c46 1.7 Protein Translation
Hsp90 ruditapes_c1528 2.5 Stress response
Glutathione
Peroxidase 3 ruditapes2_c3709 3.4 Oxidative Stress
43. Summary
• No effect of elevated pCO2 on growth or
survival
• Manila clam larvae increase transcription in
response to an elevated pCO2 environment
• Characterized biological processes impacted by
elevated pCO2
• Identified candidate genes for further study
48. Calcification and Ion Transport
Calcium carbonate abundance decreases making calcification
more difficult.
Genes associated with calcification and calcium ion transport
would increase to increase scavenging efforts of calcium ions.
Ambient CO2
Elevated CO2
Mean + SE Perlucin-6 Calmodulin
6.0 1.5
5.0
Fold Change
4.0 1
3.0
2.0 0.5
1.0
0.0 0
Week1 Week2 Week3 Week1 Week2 Week3
49. Protein Translation and Stability
Organisms respond to stress by changing gene expression and protein
synthesis.
Therefore genes involved with protein translation would also increase.
Ambient CO2
Elevated CO2
Mean + SE Cathepsin-L Elongation Factor 2
4.0 1.2
1
3.0
Fold Change
0.8
2.0 0.6
0.4
1.0
0.2
0.0 0
Week1 Week2 Week3 Week1 Week2 Week3
Cathepsin-L consistently lower though differences are not significant.
50. Stress Response
Transcription molecular chaperones and genes involved in cell
stress response increase in response to environmental stress
Ambient CO2
Elevated CO2 HSP90
Mean + SE 1.4
1.2
Fold Change
1
0.8
0.6
0.4
0.2
0
Week1 Week2 Week3
51. Oxidative Stress
Environmental stress, increases in metabolism, and cell signaling can
increase production of ROS.
Genes that catabolize ROS would therefore increase .
Ambient CO2
Elevated CO2 Glutathione Peroxidase 3
Mean + SE
1.5
Fold Change
1
0.5
0
Week1 Week2 Week3
Glutathione peroxidase 3 is lower in elevated pCO2 exposed animals at
weeks one and two but difference is not significant
52. Does this affect the response
to other stressors?
• Juvenile Manila clams do not change
transcription levels of candidate genes when
exposed to elevated pCO2.
• Do juvenile clams still possess the
physiological potential to cope with multiple
stressors when exposed to a high pCO2
environment?
53. Impact of Multiple Stressors
Hypoxia Salinity
Temperature Disease
Ocean Acidification
58. Summary
Hypothesis:
Ocean acidification will negatively impact manila clams.
59. Summary
1. No affect on larval growth and 2. Larvae increase expression of
mortality. genes involved in essential biological
processes.
150% 23000
100% 18000
50% 13000
0% 8000
1 4 7 11 14 1 4 7 11 14
3. Juvenile clams to not respond to 4. Elevated CO2 does not impact
elevated pCO2 by increasing gene thermal tolerance.
expression.
1.5
100% 100%
1 80% 80%
60% 60%
0.5 40% 40%
20% 20%
0 0% 0%
Week1 Week2 Week3 Day1Day2Day3Day4Day5Day6Day7 Day1Day2Day3Day4Day5Day6Day7
60. Impact of Multiple Stressors
Hypoxia Salinity
Temperature Disease
Ocean Acidification
61. Summary
Hypothesis:
Ocean acidification will negatively impact manila clams.
Constant exposure to changing environmental
conditions has conditioned Manila clams to effectively
cope with increasing pCO2 levels as a result of ocean
acidification
62. Future Studies
• Are other biological processes in juvenile
Manila clams impacted by OA?
• Does ocean acidification impact reproduction
and fertilization?
• Is there an effect on calcification?
63. Acknowledgements
University of Washington Friday Harbor Laboratories NOAA NWFSC
Roberts Lab: Carrington Lab: Shallin Busch
Sam White Emily Carrington Paul McElhany
Steven Roberts Moose O’Donnell Mike Maher
Emma Timmins-Schiffman Jason Miller
Caroline Storer Sarah Norberg
Mackenzie Gavery
Friedman Lab: Taylor Shellfish
Carolyn Friedman Greg Jacob
Brent Vadopalas Joth Davis
Lisa Crosson
Elene Dorfmeier Funding
Sammi Brombacker Washington Sea Grant
Robyn Strenge Saltonstall-Kennedy
University of Washington
Georgia O’Keeffe’s 1926 pastel “Slightly Open Clam Shell”
Upwelling of corrosive water has been shown to be detrimental to early developmental stages of calcifying organisms. Conseuqently, several studies have been conducted to assess the suseptability of important aquaculture species such as mussels and oysters. Results from these studies indicated that high pCO2 levels will reduce production as a result of incrased mortality and slower growth. No studies, however, have been conducted that assess the impact of ocean acidification manila clams.
Upwelling of corrosive water has been shown to be detrimental to early developmental stages of calcifying organisms. Conseuqently, several studies have been conducted to assess the suseptability of important aquaculture species such as mussels and oysters. Results from these studies indicated that high pCO2 levels will reduce production as a result of incrased mortality and slower growth. No studies, however, have been conducted that assess the impact of ocean acidification manila clams.
Upwelling of corrosive water has been shown to be detrimental to early developmental stages of calcifying organisms. Conseuqently, several studies have been conducted to assess the suseptability of important aquaculture species such as mussels and oysters. Results from these studies indicated that high pCO2 levels will reduce production as a result of incrased mortality and slower growth. No studies, however, have been conducted that assess the impact of ocean acidification manila clams.
Upwelling of corrosive water has been shown to be detrimental to early developmental stages of calcifying organisms. Conseuqently, several studies have been conducted to assess the suseptability of important aquaculture species such as mussels and oysters. Results from these studies indicated that high pCO2 levels will reduce production as a result of incrased mortality and slower growth. No studies, however, have been conducted that assess the impact of ocean acidification manila clams.
Upwelling of corrosive water has been shown to be detrimental to early developmental stages of calcifying organisms. Conseuqently, several studies have been conducted to assess the suseptability of important aquaculture species such as mussels and oysters. Results from these studies indicated that high pCO2 levels will reduce production as a result of incrased mortality and slower growth. No studies, however, have been conducted that assess the impact of ocean acidification manila clams.
Manila clam production has expanded rapidly since 1990
Temp is within range for optimal spawning and larval development
Temp is representative of optimal growing conditions
Whygil tissue? Constantly exposed to water and site of ion and gas exchange with the environment. Also rich with hemocytes which are the cells primarily involved in stress response
Increase CO2 exposure and see if that elicits more of a responseNGS on juvenilesDig deeper into larval NGS data2. Can learn a lot from these experiments but multi generation and long term monitoring are the direction research needs to be going