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Biogeochemistry of WetlandsS i d A li tiS i d A li ti
Institute of Food and Agricultural Sciences (IFAS)
Science and ApplicationsScience and Applications
Wetland Biogeochemistry LaboratoryS il d W t S i D t t
ADVANCES IN BIOGEOCHEMISTRY
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Instructor :Patrick [email protected]
Soil and Water Science DepartmentUniversity of Florida
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Characterization of specific organisms having the
gene
Characterization of specific organisms having the
gene
Cloning
Sequencing
Environmental sample
NA extraction
Molecular Approaches:Molecular Approaches:
q-PCR
PCR
DGGE t-RFLP
ggprobes
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Abundance/ expression of specific gene
Abundance/ expression of specific gene Relative abundances of
groups expressing geneRelative abundances of groups expressing gene
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Molecular Approaches:Molecular Approaches:Consortia Consortia
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c, Epifluorescence micrograph after hybridization with the general bacterial probe EUBmix (blue), the specific bacterial probe DBACT-193 (red) and the specific archaeal probe DARCH-872 (green). The bacterial partner is pink, as it hybridizes with both the general and specific bacterial probes. d, Epifluorescence micrograph after hybridization with the general archaeal probe ARCH915 (blue), the specific archaeal probe DARCH-872 (red) and the general bacterial probe EUBmix (green). The archaeal partner is pink because it hybridizes with both the general and specific archaeal probes. Scale bars, 5 m. See Methods for specification of probes.
Raghoebarsing et al. 2006. Nature 440, 918-921
• Monitored groundwater Nitrate in wells near drainage ditches
Isotopic Approaches:Isotopic Approaches:Natural Abundance Levels Natural Abundance Levels
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13CO2
13CO2
13CO2 13CO213CO2
13CO2
13C
Isotopic Approaches:Isotopic Approaches:Enriched Levels Enriched Levels
13CO2
13CO2
13CO2
13CO22
Time
C
Ti
13C
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Time
Time
13C
Isotopic Approaches:Isotopic Approaches:Enriched Levels Enriched Levels
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Buckley, et al. 2007. Appl. Env. Microbiol. 73: 3189–3195
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Cooperative relationship ?Cooperative relationship ?CO2CO2
O-O-O-O-
EPS
GlycolateALGAE
RCRC O
O-
P O-O
O-
P O-RCRC O
O-
P O-O
O-
P O-
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BACTERIAO
O-
O-
P O-O
O-
O-
P O-
18 2 6 18 3 318 1 9c
GroupGroup--Specific 13C TracingSpecific 13C Tracing(using Phospholipid Fatty Acids, PLFA)(using Phospholipid Fatty Acids, PLFA)
-500
0
500
1000
1500
time (h)
δC13
18:2w 6
-500
0
500
1000
1500
time (h)
δC13
18:3w 3
-500
0
500
1000
1500
time (h)
δC13
18:1w 9c
18:1w 5c16:1w 7c
Cyanophytes Green Algae Green Algae
Gram( ) Bacteria Gram( ) Bacteria
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-100
0
100
200
300
400
time (h)
δC13
i15:0
-100
0
100
200
300
400
time (h)
δC13
18:1w 5c
-100
0
100
200
300
400
time (h)
δC13
16:1w 7cGram(+) Bacteria Gram(-) Bacteria Gram(-) Bacteria
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Coupled Biogeochemical CyclesCoupled Biogeochemical Cycles
Mutual dependency of one cycle on another (feedbackscycle on another (feedbacks and controls) or one organism on another (microbes, algae, and vegetation)Linkages between biogeochemical processes and biotic communities (vegetation,
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( galgae, and microbes)Cycles at different scales (molecular to landscape)
Biogeochemical Biogeochemical GradientsGradients
Hydrologic gradientsy g gClimate gradientsNutrient gradientsBiotic community gradientsSpatial gradients
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Temporal gradientsScales
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Plant
Coupled CyclesCoupled CyclesEcosystem Processes: Ecosystem Processes:
Nutrient CompetitionNutrient Competition
Microbial Bi Nitrifiers Denitrifiers
Org-N NH4+ NO3
-
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Biomass Nitrifiers Denitrifiers
N2/N2O
Ecosystem Coupling: Ecosystem Coupling: Salt Marsh Nutrient Limitation?Salt Marsh Nutrient Limitation?
Plan
t
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Sundareshwar, et al. 2003. Science 299: 563 – 565.
ContCont
P
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Coupled Cycles: Coupled Cycles: Salt Marsh Nutrient Limitation?Salt Marsh Nutrient Limitation?
Control
w/ Pw/ P
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Sundareshwar, et al. 2003. Science 299: 563 – 565.
Controlw/
Glucose
Coupled Cycles: Coupled Cycles: Salt Marsh Nutrient Limitation?Salt Marsh Nutrient Limitation?
Plant
P
CNH4
+ NO3-
N-fixersN-fixers Nitrifiers Denitrifiers
P
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N2/N2O
N fixersN fixers Nitrifiers Denitrifiers
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LithologyHydrologyLand Use
Improving ModelsImproving Models
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VegetationOrganic matter
Rhizosphere interactions
Improving ModelsImproving Models
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Improving ModelsImproving Models
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Photos courtesy of G. W. Hurt
WELL-DRAINED SOIL
Fe3+ Mn4+
Improving ModelsImproving Models
RECENTLY DRAINED
AerobicAnaerobic
Mn2+Fe2+Mn2+
Fe2+
Fe3+Mn4+
RECENTLY FLOODED
AerobicAnaerobic
Mn4+Fe3+Mn2+
Fe2+
Fe3+Mn4+
Aerobic
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AerobicAnaerobic
FLOODED FOR LONG PERIOD
Mn2+Fe2+
Anaerobic
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Improving ModelsImproving Models
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Real-Time Datahttp://hudson.dl.stevens-tech.edu/maritimeforecast/maincontrol.shtml
05:00
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08:00
11:00
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The FutureThe Future
Identification of organism d th di itand pathway diversity
Refine methods to partition and trace element flowsIntegrate the concepts of coupled cycles into our temporal and landscape
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temporal and landscape models Real time simulations/predictions