Download Connectivity of Earth`s largest biomes: the deep Atlantic to the

Traditional and emergent molecular techniques
to characterize species biodiversity and
ecosystem health (plus a bunch of other stuff)
Heather Bracken Grissom
Florida International University
Tracey Sutton, Kevin Boswell, April Cook, Sergio deRada, David English, Ron Eytan,
Danté Fenolio, Tamara Frank, Chuanmin Hu, Heather Judkins, Chad Lembke, Joseph
Lopez, Jon Moore, Martha Nizinski, Brad Penta, Isabel Romero, Jay Rooker, Mahmood
Shivji, Michael Vecchione, David Wells, Marsh Youngbluth
Mission Statement
• The DEEPEND consortium will characterize the
oceanic ecosystem of the northern Gulf of
Mexico to infer baseline conditions in the
water column.
• This information will establish a time-series
with which natural and anthropogenic
changes can be detected.
Objective 1: How does oceanic
biodiversity vary with space and time?
Photos: Fenolio, Frank, Shale, Youngbluth, and Zankl
DEEPEND field sampling technology
surface
200 m
600 m
1000 m
1200 m
1500 m
• R/V Point Sur
• 10-m2 MOCNESS
Biodiversity and Community Structure
Alpha taxonomy
Tracey Sutton, Jon Moore, Ted
Pietsch, Chris Kenaley, Dave
Johnson, John Paxton
DEEPEND Imaging Project:
Danté Fenolio (SAZ)
Biodiversity and Community Structure
Alpha taxonomy
Tammy Frank (NSU), Martha Nizinski (NOAA),
Heather Bracken-Grissom (FIU), Heather
Judkins (USFSP), Mike Vecchione (NOAA),
Marsh Youngbluth (HBOI-FAU)
Genetic Taxonomy
Using DNA Barcoding Methods to document biodiversity and
create species inventories
Ron Eytan (TAMU), Mahmood Shivji (NSU), Joe Lopez (NSU),
Heather Bracken-Grissom (FIU), Heather Judkins (USFSP)
DNA Barcoding
• Method used to identify organisms
• Much like assigning a “numerical barcode” to
shopping item
• Sequence a ~600 base pair segment of DNA
to reveal an organism “barcode”
• Organisms have unique DNA sequences for
each species
DNA Barcoding
•
•
•
•
•
Protocol
Extracted DNA from muscle tissue
PCR amplification
DNA sequencing
Selected genes with enough variation to
detect species-level differences (COI, 16S)
To date: 400 species fish, 100 species of
crustaceans, 20 species of cephalopods
http://ccdb.ca/research.php
Why Barcode?
• Allows us to identify organisms based on DNA
sequences and create species inventories
– Useful in discovery of new species OR when specimen is
damaged, mutilated or identity is unknown/uncertain
• Allows us to make larval-adult linkages
– Useful when larval forms differs from adult counterpart
– Provides insights into the ecology and life history of the
species
– Example = Cerataspis monstrosa (Bracken-Grissom et al. 2012)
Adult
Larval form
From Barcoding to Ecosystem Health,
Recovery and Resilience
Objective 2: Are there longer-term consequences of
DWHOS on the pelagic communities?
~ 1500 m
http://www.maritime-executive.com/article/Macondo-Accident-25-Miles-of-Seafloor-Oil-2014-10-27
Photos:Fenolio
Using genetic information, we are able to establish
and measure proxies for health and resilience of an
ecosystem.
Genetic Diversity (GD) is a
proxy for ecosystem health
Connectivity is a proxy for
ecosystem resilience
Spain
Hughes et al., 2008
Black lines = direct ecological consequences of GD
Dotted lines = indirect ecological consequences of GD
Mullus surmuletus, Felix-Hackradt et al. 2013
How do we measure genetic diversity
and connectivity?
• Comparisons will be made across populations
within a species across time and space
• Extract DNA from ~20-30 individuals per
population
• Recent advancements in DNA sequencing
technology allows us to “scan” the entire
genome
• Method called: Double Digest Restriction site
associated DNA Sequencing or ddRADSeq
RADseq Protocol
1. Digest the genomic DNA with restriction
enzymes
1.
2. Attach a short “barcode” sequence that
will allow you link the piece of DNA to an
individual or species
2.
3. Do this multiple times throughout the
genome and for many individuals (pool
samples)
4. Sequence the DNA on a next-generation
sequencing platform (ex. Illumina)
5. Run an analysis that will allow you to
compare all the same pieces of DNA.
Identify DNA difference across the entire
genome (1000s-10,000s basepairs)
3.
4.
5.
Genetic Diversity will be compared
across temporal and spatial scales
Total (2010-2011): 235 sea-days, 1580 samples (Gulf of Mexico
Offshore Nekton Sampling and Analysis Program)
Total (2015-2017): 78 sea-days, TBD samples (DEEPEND)
NOAA FSV Pisces
M/V Meg Skansi
6 species of fish, 9
species of
crustaceans and 3
species of
cephalopods have
been targeted
Do we see evidence for changes in GD pre- and post spill?
Document the natural variation in GD across temporal scales?
Connectivity studies are underway to
study resilience and recovery of GoM
Bear Seamount,
N. Atlantic
FL Straits
Gulf of Mexico
Additional DEEPEND field sampling
technology
DEEPEND field sampling
Plankton
• M/V Blazing Seven
• Neuston/bongo nets
DEEPEND field sampling
MOC10/Oceanography
Cruise track
Stations and
watermasses
DEEPEND cruise DP01 – May 2015
212 fish spp.
Astronesthes sp. nov.
Community Structure and Numerical
Transducer
Modelling
Bio-acoustic Oceanography
Kevin Boswell (FIU) Joe Warren (Stony Brook)
250
500
750
Example of the mesopelagic layers that move between day and night. The highest density of
animals is displayed in red and the lowest density is shown in dark blue. The microscopic view
from the SONAR on the CTD shows the individuals that live in these migrating layers.
Community Structure and Numerical
Modelling
Meso-Scale Oceanography
Community Structure and Numerical
Modelling
Meso-Scale Oceanography
Chuanmin Hu, Dave English, Chad Lembke (USF)
Isistius plutodus, GoM 2011
Please visit us at:
www.deependconsortium.org
THANK YOU!