Methods in Microbial Biogeochemistry, 5

Credits, 11.-26.5.2017
Thursday, 11.5.2017
GOALS: - Introduction to the course, formation of groups (Christina, Henri)

WHERE: SN 206

TIME/GOAL INTRO

8:15-9:15

9:15-10:15

10:15-11:30

11:30-13:00 LUNCH

13:00-14:00 Seminar SN 206

14:00-15:00 Seminar SN 206

14:30-16:00

Friday, 26.5.2017

GOALS: - Collection of gas and soil samples from peatland and forest
soils (Richard, Henri, Jukka, Marja, Maija, Christina). Chapter 3.1.

WHERE: near Suonenjoki, we meet at 8:15 in SN 206!

Collection of
TIME/GOAL
samples

8:15-9:15 FIELD TRIP

9:15-10:15 FIELD TRIP

10:15-11:30 FIELD TRIP

11:30-12:30 LUNCH

12:30-13:30 FIELD TRIP

13:30-14:30 FIELD TRIP

14:30-16:00 FIELD TRIP

Monday, 15.5.2017
GOALS: - Soil homogenization, start of basic soil characteristics (Hannu, Christina) - chapter 3.1.-3.7.
- start of methane production/oxidation experiment (Christina, Henri) - chapter 4 -
sample preparation for DNA extraction (Richard, Henri, HemRaj) - chapter 5

WHERE: Biogeochemistry labs

Methane
Soil Soil for DNA
TIME/GOAL Producation/oxidation
Homogenization Extraction
potential

8:15-9:15 Lecture SN 400

9:15-10:15 G1, G2, G3

10:15-11:30 G1, G2 G3

11:30-12:30 LUNCH LUNCH LUNCH

12:30-13:30 G3 G1, G2

13:30-14:30 G1. G2, G3

14:30-16:00 G1, G2, G3

Tuesday, 16.5.2017
GOALS: - soil properties continued (Hannu) - chapters 3.1-3.7 -
Soil DNA extractions (Richard, Henri, HemRaj) - chapter 5
- Sampling for methane production/oxidation potential (Maija, Henri) - chapter 4

WHERE: Biogeochemistry labs and SN209A

Methane
Soil DNA Soil properties (SN
TIME/GOAL Producation/oxidation
Extraction 4137)
potential

8:15-9:15 Lecture SN 400

9:15-10:15 G1, G2, G3

10:15-11:30 G1, G2 G3

11:30-12:30 LUNCH LUNCH LUNCH

12:30-13:30 G3

13:30-14:30 G1, G2

14:30-16:00 G1, G2, G3

Wednesday, 17.5.2017
GOALS: - DNA purification and concentration measurements with NanoDrop (Richard, Henri, HemRaj) -
chapter 5 -
Quantification of methanogens (Richard, Henri, HemRaj) - chapter 5

WHERE: Biogeochemistry labs and SN209A

Quantification of
TIME/GOAL DNA purification methanogens and
methanotrops

8:15-9:15 Lecture SN 400

9:15-10:15 G1. G2, G3 G1. G2, G3

10:15-11:30 G1. G2, G3 G1. G2, G3

11:30-12:30 LUNCH LUNCH

12:30-13:30 G1. G2, G3 G1. G2, G3

13:30-14:30 G1. G2, G3 G1. G2, G3

14:30-16:00 G1. G2, G3 G1. G2, G3

Thursday, 18.5.2017
GOALS: - Agarose gel electrophoresis (Richard, Henri, HemRaj) - chapter 5
- Calculation of gene copy numbers; ligation and transformation to E. coli (Richard, Henri, HemRaj) -
chapter 5

WHERE: Biogeochemistry labs and SN209A

Calculation of gene
Agarosie-gel
TIME/GOAL copy numbers,
electrophoris
ligation/transformation

8:15-9:15 Lecture SN 400

9:15-10:15 G1, G2

10:15-11:30 G3

11:30-12:30 LUNCH LUNCH

12:30-13:30 G1. G2, G3

13:30-14:30 G1. G2, G3

14:30-16:00 G1. G2, G3

Friday, 19.5.2017
GOALS: - Amplification of colonies after transformation (Richard, Henri, HemRaj) - chapter 5
- (Agarose gel electrophoresis of PCR products )

WHERE: Biogeochemistry labs and SN209A

Agarose-gel
TIME/GOAL Colony PCR
electrophoresis

8:15-9:15 Lecture SN 400

9:15-10:15 G3

10:15-11:30 G1, G2

11:30-12:30 LUNCH LUNCH

12:30-13:30 G1. G2, G3

13:30-14:30 G1. G2, G3

14:30-16:00 G1. G2, G3

Monday, 22.5.2017

GOALS: - Standard preparation for GC, GC preparation for analysis (Marja) --

Measurement of gas concentrations from field and lab (Marja)

WHERE: Biogeochemistry labs

Standard
TIME/GOAL GC measurements
preparation

8:15-9:15 Lecture SN 400

9:15-10:15 G1, G2, G3

10:15-11:30 G1, G2, G3

11:30-12:30 LUNCH LUNCH

12:30-13:30

13:30-14:30

14:30-16:00
Tuesday, 23.5.2017
GOALS: - Calculation of soil GHG fluxes (Marja, Christina) - chapters 2.4-2.6 -
Calculation of methane production/consumption potential and soil properties (Maija, Henri, Hannu,
Christina)

WHERE: CA 103

Soil GHG fluxes, Methane

Soil properties -
TIME/GOAL soil properties, production/oxidation
CALC
CALC CALC

8:15-9:15 CA 103

9:15-10:15 CA 103

10:15-11:30 CA 103

11:30-12:30 LUNCH LUNCH

12:30-13:30 CA 103

13:30-14:30 CA 103

14:30-16:00 CA 103

Wednesday,
24.5.2017

GOALS: - Calculation and plotting of qPCR data (Henri, Richard, HemRaj) - chapter 5
- perparation of presentation

WHERE: CA 103
Quantification of Preparation of
TIME/GOAL
gene data, CALC presentation

8:15-9:15 CA 103

9:15-10:15 CA 103

10:15-11:30 CA 103

11:30-12:30 LUNCH LUNCH

12:30-13:30 CA 103

13:30-14:30 CA 103

14:30-16:00 CA 103
Thursday, 25.5.2017 PUBLIC HOLIDAY

Friday, 26.5.2017

GOALS: - presentation of course results by the students

WHERE: SN 400
TIME/GOAL Presentation

8:15-9:15

9:15-10:15 Seminar SN 400

10:15-11:30 Seminar SN 400

11:30-12:30 LUNCH

12:30-13:30 Seminar SN 400

13:30-14:30 Seminar SN 400

14:30-16:00