oceanic microbial observatory sar11 (e5/l). 1. 1.identify spatial and temporal patterns in specific...
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Oceanic Microbial ObservatoryOceanic Microbial ObservatoryQuickTime™ and a
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SAR11 (E5/l)
1. Identify spatial and temporal patterns in specific bacterioplankton/ prokaryotic populations
2. Initiate experiments to investigate potential linkages between microbial processes, community structure and biogeochemical processes / events.
3. Discovery…. High throughput culturing in low nutrient media as a means to bring some of the uncultured bacterioplankton - into culture
4. Education and Outreach
Oceanic Microbial Oceanic Microbial ObservatoryObservatory ObjectivesObjectives
16 cruises / yr16 cruises / yr
Core Measurements
TemperatureTemperature SalinitySalinityDissolved OxygenDissolved Oxygen FluorescenceFluorescenceBeam AttenuationBeam Attenuation PARPAR
SalinitySalinity Oxygen OxygenTotal COTotal CO22 (TCO (TCO22)) AlkalinityAlkalinity
NitrateNitrate Nitrite NitritePhosphate Phosphate SilicateSilicatePOC/PONPOC/PON DOC/DON DOC/DONPigments (HPLC)Pigments (HPLC) Bacteria Bacteria
Primary ProductionPrimary ProductionBacteria ProductionBacteria Production
Particle FluxesParticle Fluxes
Discrete
Continuous
Rates
1988 - present1988 - present
Temperature and mixed layer depth at BATSD
epth
(m
)0
50
100
150
200
250
3001989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999
Tem
p. (
°C)
30
29
28
27
26
25
24
23
22
21
20
19
18
BATS CoreBATS Core
Bacterial Biomass
Bacterial Production
µ
• BP - estimated via 3H-TdR incorporation
• Summer max in BP and µ
Composite of Bacterial biomass and production
integrated throughout the Euphotic zone at BATS
Steinberg, Carlson, Bates et al. 2001Steinberg, Carlson, Bates et al. 2001
0
50
100
150
200
250
300
12
10
8
6
4
2
0
91 92 93 94 95 96 97 98 99 00
Prokaryotic Cell Abundance (cells E8 l-1)D
epth
(m
)
1000
900
800
700
600
500
400
300
200
100
00 1 2 3 4 5 6 7 8 9 10
Dep
thCells E8 / l
1
10
40
60
80
100
150
250
500
1000
Bacterial LH-PCR 16s electropherograms
BATS CDOM Cruise Aug 2001
• • 10 m or 250 m whole water 10 m or 250 m whole water was diluted 0.22µm filtrate was diluted 0.22µm filtrate from surface or 250 mfrom surface or 250 m
• • Cultures were incubated at Cultures were incubated at inoculum’s in situ inoculum’s in situ temperatures in the dark temperatures in the dark
Mixing Experiments
MO Objective: investigate potential linkages between microbial processes, community structure and biogeochemical patterns
50
55
60
65
70
DO
C (
µM
C)
Niskin
Day 1
Day 7
Day 37
0
0.1
0.2
0.3
0.4C
ells
E9
/ l
Surf / Surf 0.2 µm Deep/ deep 0.2µm
Surface / surface 0.2µ
treatment
Deep / deep 0.2µ treatment
Deep/ surf 0.2 mediab a50
55
60
65
70
0
0.1
0.2
0.3
0.4
0 1 2 3 4 5 6 7
Cel
ls E
9/l
DO
C (
µM
C)
Surf / mix 0.2 µm
Surface /(surf+deep) 0.2µ
Deep / Surf 0.2µ
HS 893 Mixing ExperimentHS 893 Mixing Experiment
0 1 2 3 4 5 6 7
daysdays Carlson et al. 2004Carlson et al. 2004
Experiment Inoc. 0.2 Filtrate ∆Cell ∆DOCSource Source Cells E8/l 1 week > month
HS 852 (Aug-97) Surf Surf 0.75 - -
Deep Surf 2.85 1.9 3.5
HS 875 (Aug-98) Surf Surf 0.75 - -
Deep Surf 2.5 3.1 3.1
HS 893 (Aug-99) Surf Surf 0.5 - -
Deep Surf 2.1 3.7 5.1
Deep Deep 0.25 - -
Surf mix 0.9 - 1.3
BATS 155 (Aug-01) Surf Surf 0.5 - -
Deep Deep - - -
MLD and Integrated Prokaryotic Biomass in the Upper MLD and Integrated Prokaryotic Biomass in the Upper
Mesopelagic at BATSMesopelagic at BATS
Identification of Terminal Restriction Fragments
TRFLP
Groups
Fragment length observed
Fragment length predicted
from sequence
Sequence Identification
1 113, 226, 290 117, 228, 294 SAR11, 33
2 115, 193 119, 193 Unc. Gamma, 9
3 194 195 Roseobacter
4 302 303 OCS 116, 4
5 155, 260 158, 263 SAR202, 3
6 405 405 SAR324, 2
7 303, 388 304, 390 Prasinophytes, 2
8 328 330 Marine Actinobacteria
9 192 193 SAR116
164 samples from 1992 -2002
81 - surface samples
83- 200 m samples
HAE III- digest 27F, 519 R
Ordination of T-RFLP Fragments (1992-2002)Nonmetric multidimensional scaling
Morris,Cho, Rappé, Vergin, Carlson, and Giovannoni, In Press
Roseobacter (E5/L)
Cytophaga-Flavobacteria (E5/L)
SAR 11 (E5/L)
Carlson, Morris, Parsons and Giovannoni, unpublished
MO objective: Identify spatial and temporal patterns in specific bacterioplankton/ prokaryotic
populations
FISH DATA
OSU High Throughput Cultivation Lab>2000 Strains
> 80% do not grow on agar18 strains in genome sequencing
Natural Sample
Dilute cells and distribute into wells of microtiter dishes
Step 1: Dilution to extinction
Step 2:Cell Arrays
Cells arrayed on polycarbonate membranes
Target species identified by multiplexed in situ Hybridization and laser scanning cytometry
Step 3: High-Throughput Cell Identification
MO Objective: Isolation of new organisms
Courtesy of S. Giovannoni
Marine Microbial EcologyMarine Genomics
http://www.lifesci.ucsb.edu/~carlson/
MO objective: Education & Outreach
Acknowledgements BBSR
Rachel Parsons
Nick Bates
Rod Johnson
Mike Lomas
Tony Michaels
Dennis Hansell
Debbie Steinberg
Norm Nelson
Tony Knap
BATS Team past and present
UCSB
Stu Goldberg
Courtney Ewart
Kurt Gray
Elli Wallner
Aubrey Cano
Meredith Meyers
OSU
Steve Giovannoni
Kevin Vergin
Bob Morris
Mike Rappé
Giovannoni Lab group