si da li ti science and applications advances in ......4 13co 2 13co 2 13co 2 13co 2 13co 2 13co 2...

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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 Inglettpinglett@ufl.edu

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

6/22/2008 P.W. Inglett 16Sundareshwar, et al. 2003. Science 299: 563-565.

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