Transcript Dynamics of nitrogen cycling microorganisms in the open - C-MORE

The Ecology of Nitrogen Cycling
Microorganisms in the Subtropical
North Pacific Ocean
Thank you…
 Daniela Böttjer, Brenner
Wai, Donn Viviani, Sara
Thomas, Christina
Johnson
 Dave Karl, Jon Zehr, Ed
DeLong
NSF
A Dedicated HOT Team
NSF
NSF
N cycle stories from the open sea
 How do seasonal to episodic changes in the upper
ocean habitat influence distributions, abundances,
and activities of N cycling microorganisms?


N2 fixing cyanobacteria
Ammonia oxidizing Crenarchaea
Focus on epipelagic N- cycle dynamics:
 Concentrations of inorganic N low
 Rapid N turnover
 Intense vertical gradients in microbial habitat structure
(light, nutrients, temperature, etc.)
 Sensitive to physical perturbations (seasonal to episodic)
Time, water, and change
 The 24 years of Hawaii
ALOHA
Ocean Time-series (HOT)
measurements provide a
rich time-history for
assessing change to a
persistently oligotrophic
ocean ecosystem.
provides insight into the
mean ecosystem state,
and variability around
the mean state.
Photo: Paul Lethaby
 The resulting data
The upper ocean habitat
PAR (mol quanta m-2 s-1)
100
101
102
14
C-PP (mol C L-1 d-1)
103
0
0.0
0.1
0.2
0.3
0.5
0.6
0
14C-PP
PAR
50
Depth (m)
0.4
MLD
100
50
100
1%
Chl a
150
150
N+N
200
0.1%
200
0
1
2
3
4
5
-1
Nitrate + Nitrite (mol N L )
0.0
0.2
0.4
0.6
Chlorophyll a
-1
(g L )
0.8
Physical and biological controls on
nitrogen availability to the upper ocean
 Physical:
 Mixing
 Upwelling, downwelling
 Biological:
N2 fixation
NH4+
Organic
matter
N2 fixation
Remineralization
(e.g. ammonification,
nitrification)
These processes
are time variable
Organic
matter
NH4+
NO3-
NO3-
NO2-
NO2-
Organic
NH4+ matter
ML temp (oC)
26
25
24
23
60
40
105
104
103
102
Month
Dec
Nov
Oct
Sept
Aug
July
Jun
May
Apr
Mar
Feb
101
Jan
Nitrate (mol N m-2)
20
Irradiance
(mol quanta m-2 d-1)
Seasonal
variations in
upper ocean
temperature,
light, and
nutrients
27
C-prim. prod.
(mmol C m-2 d-1)
-1
(mmol C m d )
3.5
-2
3.0
50
40
14
30
20
2.5
2.0
1.5
Jan
Feb
Mar
Apr
May
Jun
Jul
Aug
Sep
Oct
Nov
Dec
Productivity and
export both
elevated in
summer when
upper ocean
nutrient
concentrations
are lowest.
Carbon export
Seasonal
climatology of
primary
production
and particle
export
60
What processes supply nitrogen to support new production in this ecosystem?
Biological N supply to the ocean:
N2 fixation
 At ALOHA, N2 fixation fuels ~50% of new production
(and hence carbon export)
 Several groups of N2 fixing microorganisms identified
 Regular occurrence of large blooms of N2 fixing
microorganisms; Trichodesmium spp. and/or
diatoms with endo/epi-symbionts
 Changes in elemental stoichiometry of particulate
and dissolved nutrient pools (decreased P
availability) attributed to N2 fixation.
Motivating Questions
 How variable in time are N2 fixing microbes and
rates of N2 fixation?
 What processes control variability in diazotroph
population structure and rates of N2 fixation?
Approach
Combined rate measurements of N2
fixation together with analyses of
time/space variability in
distributions and activities of N
cycle microbes in the sea.
nifH → Nitrogenase (N2 fixers)
N2 fixing cyanobacteria
at Station ALOHA based
on nifH gene transcripts
Richelia-1
Richelia-2
Richelia-120-50 m
Heterocystous
cyanobacteria
Richelia-1
>10 m
Richelia-2
Calothrix
2-10 m
Group A
Unicellular
cyanobacteria
Crocosphaera
Trichodesmium /
Katagynemene
Calothrix
20-50 m
Trichodesmium spp.
Katagynemene spp.
Images courtesy of
Angel White, Rachel Foster,
Grieg Steward
20-100 m
2-2000 m
Crocosphaera
“Group A”
Several cultivated strains (in culture since 1985)
Uncultivated
Fixes N2 at night
Likely fixes N2 during day
Photosystem I & II
Photosystem I
Functional TCA cycle
No TCA cycle
Photoautotroph
Photoheterotroph
“Free” living
Symbiont?
Crocosphaera
106
105
104
103
Church et al. (2005)
Time
10:00
04:00
22:00
16:00
10:00
04:00
22:00
16:00
10:00
04:00
102
22:00
nifH expression
( transcripts L-1 )
Group A
Crocosphaera
0-125 m
05
06
07
08
09
10
1012
1011
1010
109
108
107
106
1012
1011
1010
109
108
107
106
Crocosphaera
(nifH genes m-2)
1012
1011
1010
109
108
107
106
Crocosphaera
(nifH genes m-2)
Group A
(nifH genes m-2)
Group A
11
1012
1011
1010
109
108
107
106
Jan
Feb
Mar
Apr
May
Jun
Jul
Aug
Sep
Oct
Nov
Dec
Group A
(nifH genes m-2)
Year
Abundances of unicellular N2 fixing cyanobacteria vary seasonally and interannually
Temporal variability in N2 fixation
(mol N m-2 d-1)
N2 fixation
400
0-125 m
Whole SW
<10 m
300
200
100
0
2006
2007
2008
2009
2010
2011
Year
• Major fraction (~70%) of annual N2 fixation
associated with microorganisms <10 m.
• Rates of N2 fixation tend to increase in the summer,
driven by microorganisms > 10 m.
nifH genes
-2
(copies m )
Filamentous
Unicellular
0-125 m
1011
1010
109
108
Filamentous
diazotrophic
cyanobacteria
increase
episodically
through the
summer and fall
107
< 10 m
300
-2
200
100
Modified from Church et al. (2009)
Dec
Nov
Oct
Sept
Aug
July
June
May
Apr
Mar
Feb
0
Jan
N2 fixation
-1
(mmol N m d )
Whole SW
Unicellular N2
fixers are dominate
diazotroph
abundances and
activities most of
the year
Spatiotemporal history of a
downwelling eddy
Fong et al. 2008
January 2005
April 2005
0
July 2005
July 2005
Depth (m)
50
100
“typical
profile”
150
200
0.0
0.2
0.4
0.6
0.8
Chloropigment (g L-1)
1.0
Episodic
increases in N2
fixation by
diazotrophs >10
m appear
associated with
mesoscale
physical forcing
Temperature (oC)
28
26
24
22
20
-15 -10
0
5
10
15
20
15
20
28
26
24
22
20
-15 -10
-5
0
5
10
SSHa (cm)
10
Modified from Church et al. (2009, GBC)
-5
<10m Seawater
Temperature (oC)
Time series
measurements
of nearsurface ocean
N2 fixation at
Station
ALOHA
Whole Seawater
5
2
1
nmol N L-1 d-1
0.5
0.2
Chlorophyll a
N2 fixing microorganism biomass accumulation
SSHa
2 white transects
Guidi et al. 2012
Property
(0-200 m)
SSHa
-
SSHa
+
Primary production


Carbon export


NO3-


NO3- : PO43-


Chl a


Prochlorococcus


Diatoms


Pelagophytes


Haptophytes


N2 fixation


What is the time history associated with these processes?
How does such mesoscale variability influence plankton ecology?
Variability in diazotrophs and N2 fixation
 Unicellular N2 fixing microorganisms are important
contributors to the upper ocean N cycle
 Different groups of N2 fixing microorganisms have very
different physiologies and population dynamics
 Larger, filamentous N2 fixing microorganisms
(Trichodesmium, heterocystous N-fixers) increase
seasonally, but episodically
 Mesoscale physical processes appear important drivers of
episodic N2 fixation supported plankton blooms
Nutrient recycling:
Dynamics of ammonia
oxidizing Thaumarchaea
amoA gene as a
molecular marker to
examine the
time/space variability
in Thaumarchaeal
distributions and
transcriptional
activities
N2 fixation
NH4+
Organic
matter
Organic
matter
NH4+
amoA
NO3-
NO3-
NO2-
NO2-
Organic
NH4+ matter
Nitrification and ammonia oxidation
 Nitrification is the two-step process that converts ammonia
to nitrate.
 Ammonia oxidation: NH3 + O2 → NO2− + 3H+ + 2e Nitrite oxidation: NO2− + H2O → NO3− + 2H+ + 2e Different steps are mediated by different groups of
prokaryotic microorganisms
 Ammonia oxidation historically thought to be catalyzed by
ammonia oxidizing bacteria (b and g-Proteobacteria)
 Now thought to be predominately driven by members of the
Thaumarchaeota (previously classified as mesophilic
Crenarchaeota).
Könneke et al. (2005)
Karner et al. (2001)
 Archaea first identified in seawater in
1992
 Found to dominate plankton biomass
in the meso- and bathypelagic waters at
Station ALOHA
 Sequencing efforts in Sargasso Sea
discovered gene encoding ammonia
monooxygenase from planktonic
Thaumarchaea (Venter et al. 2004)
 Isolation of marine Thaumarchaea
(Nitrosopumilus maritimus) from Seattle
Aquarium found to grow using ammonia
as sole source of energy, CO2 as carbon
source
“Upper ocean” Thaumarchaea
Only cultivated
representative of
marine
Thaumarchaea
“Deep ocean” Thaumarchaea
 Comparison of Thaumarchaea amoA genes indicates at least two
vertically partitioned groups (upper and deep ocean) –
Mincer et al. (2007), Beman et al. (2008).
 At Station ALOHA there appear to be “sub-clades” of these vertically
partitioned major groups.
Crenarchaea amoA genes
(copies L-1)
-1
Chl a (g L )
0.0
0.2
0.4
 Vertical
distributions of
these major
groups are
distinct, with the
transition region
between the
euphotic zone
and the upper
mesopelagic
comprising a
dynamic
transition point.
Chl a
NO2
10
Depth (m)
102 103 104 105 106 107 108
0.6
100
1% PAR
0.1% PAR
1000
0
20
40
60
80 100
Nitrite (nmol N L-1)
Upper ocean
Deep ocean
Brenner Wai, Christina Johnson
Distributions of Thaumarchaea amoA genes appear
sensitive to upper ocean mixing
0
Depth (m)
50
100
150
200
2007
2008
2009
amoA genes L-1
108
107
106
105
104
103
102
2010
Year
What processes control the vertical distributions of
Thaumarchaea?
Physics (mixing, upwelling, downwelling)?
Light?
Competition for substrates?
Top down (predators, viruses)?
Brenner Wai et al.
Thaumarchaea
amoA expression
and rates of
ammonia oxidation
at Stn. ALOHA
 Transcription of
the amoA gene
often peaks in the
transition zone
between the
euphotic zone and
the upper
mesopelagic
Ammonia oxidation rates courtesy of Mike Beman
Crenarchaea amoA abundance
transcripts per gene
(genes L-1)
103 104 105 106 107 108
10-2 10-1 100 101 102
0
Depth (m)
25
50
75
100
125
150
175
103 104 105 106 107 108
Crenarchaea amoA expression
(transcripts L-1)
Gene abundances increase by ~1000-fold between the near-surface ocean
and the lower euphotic zone (200 m).
Gene transcripts increase ~10- fold toward the base of the euphotic zone.
Why are the upper ocean populations apparently so active, yet not
abundant?
Conclusions
Time-varying changes in ocean
habitat structure influence the
population dynamics of N cycling
microorganisms.
Ecology matters: Changes in
population structure of N cycling
microbes are directly influence
ocean biogeochemistry.
Interactions between
biogeochemistry and ecology
occur across a range of scales,
from decadal to seasonal to
episodic.