Impact of fermented organic fertilizers on in-situ trace gas fluxes and on soil bacterial denitrifying communities in organic agriculture [Elektronische Ressource] / vorgelegt von Kristina Schau

Informations

• Publié par: justus-liebig-universitat_giessen
• Publié le: 01 janvier 2007
• Nombre de lectures: 8
• Langue: English
• Poids de l'ouvrage: 4 Mo

Extrait

JUSTUS-LIEBIG-
UNIVERSITÄT
GIESSEN


Institut für Angewandte Mikrobiologie



Impact of Fermented Organic Fertilizers on in-situ Trace Gas
Fluxes and on Soil Bacterial Denitrifying Communities
in Organic Agriculture


Dissertation zur Erlangung des
Doktorgrades der Naturwissenschaften
(Dr. rer. nat.)

dem Fachbereich
Agrarwissenschaften, Ökotrophologie und Umweltmanagement


und der Gemeinsamen Kommission Naturwissenschaften


vorgelegt von
Kristina Schauß


Giessen, im Juli 2006






























For my Family

Acknowledgements

First of all, I like to thank my supervisor Prof. Sylvia Schnell for giving me the opportunity to work
on this project in her lab. I enjoyed being a part of your group and greatly appreciate your
confidence in me, the fact that your door was always open to discuss my project and other
things, the possibility to attend international conferences, especially overseas, and your
support over the years, particularly in difficult times…

I also like to thank Prof. Hans-Jürgen Jäger for agreeing to review my thesis.

Special thanks to my advisor Dr. Stefan Ratering for introducing me to the ins and outs of gas
chromatography; it was very reassuring to have someone at hand familiar with its various
quirks! Thank you for being available at all hours of the day to discuss my results or proofread
abstracts and reports, and for all your help in rescuing me from random computer gremlins
that materialized on occasion at my minus touch.

For invaluable technical support I am indebted to Jan Rodrigues Fonseca who took countless
air and soil samples, rain or shine, at the field site located 50 km from the Institute. The
different analyses of various soil samples and especially the realization of the anoxic MPN
dilution series would not have been possible without the excellent technical assistance of
Jan, Rita Geißler-Plaum, Sylvia Saßmann, Renate Baumann, and several trainees. Thank you!

Many thanks to Stefanie Schump, Kathrin Thummes, Kerstin Fallschissel, Dr. Udo Jäckel, Rita
Schäfer, and Jenny Schäfer for your input and help. I appreciated our discussions and your
lending a listening ear... My time at the Institute would have been very dull indeed had I not
been surrounded by such a caring and “breakfast-loving” group of people!

I like to thank Walter Stinner and Arno Deuker, Ph.D. students of the Professorship for Organic
Farming, for our collegial working relationship during the project. It was a pleasure to work
with both of you, and I wish you all the best for your respective theses.

I am grateful to Dr. Christoph Müller for his support measuring soil denitrifying enzyme activities
and his proofreading of the English-language version of my thesis. I really enjoyed our
afternoon coffee breaks and the two conferences we attended!

And finally I like to thank my parents and my siblings Astrid, Thorsten, and Mareike for their
unfailing support over the years. Your willingness to accompany me to take gas samples
during the weekend - i.e. our day trips to lovely Aumenau in the Lahn valley - and especially
your encouragement and moral support during down times were absolutely invaluable!

Table of Contents I
Table of Contents
1 Introduction...................................................................................................................................... 1
1.1 Organic Agriculture ........................................................................................................................1
1.2 Anaerobic Fermentation in Biogas Plants ...................................................................................3
1.3 Trace Gas Fluxes in Agriculture .....................................................................................................4
1.4 Nitrous Oxide Emissions in Arable Soils..........................................................................................5
1.4.1 Denitrification ..........................................................................................................................6
1.4.2 Nitrification...............................................................................................................................8
1.5 Methane Fluxes in Arable Soils ....................................................................................................10
1.5.1 Methane Oxidation......10
1.5.2 Methane Production............................................................................................................11
1.6 Objectives and Setting of the Study ..........................................................................................12
2 Material and Methods................................................................................................................... 14
2.1 Experimental Site.................14
2.1.1 Experimental Design of the Cropping System without Livestock..................................16
2.1.2 Experimental Design of the Cropping System with Livestock........................................17
2.2 Field Trial..........................................................................................................................................19
2.2.1 In-situ Gas Flux Measurements............................................................................................19
2.2.2 Soil Mineral Nitrogen Measurements .................................................................................22
2.3 Incubation Experiments................................................................................................................22
2.4 Greenhouse Studies......................................................................................................................22
2.5 Investigations of Field Soil Samples after 3.5 Years of Different Manuring ...........................23
2.6 Chemicals, Gases, and Water ....................................................................................................24
2.7 Gas Chromatographic Analyses ................................................................................................24
2.7.1 Gas Samples of 50 ml Volume24
2.7.2 Gas Samples of 1 ml Volume or Less25
2.8 Chemical-Physical Analyses of Environmental Samples.........................................................25
2.8.1 pH-Value ................................................................................................................................25
2.8.2 Water Content ......................................................................................................................25
2.8.3 Water Holding Capacity .....................................................................................................26
2.8.4 Mineral Nitrogen ...................................................................................................................26
2.8.5 Total Nitrogen........................................................................................................................26
2.8.6 Total Carbon and Total Nitrogen .......................................................................................26
2.8.7 Microbial Biomass Carbon ..................................................................................................26
2.8.8 Water Extractable Carbon.27
2.9 Microbial Analyses of Environmental Samples .........................................................................27
2.9.1 Potential Denitrifying Activity..............................................................................................27
2.9.2 Potential Nitrifying Activity...................................................................................................27
2.9.3 MPN of Nitrate Reducing Bacteria ....................................................................................28
2.9.4 Basal Respiration...................................................................................................................29
2.9.5 Substrate Induced Respiration, SIR30
2.9.6 BIOLOG Substrate Utilization Test .......................................................................................30
2.10 Molecular Biological Analyses ..................................................................................................31
2.10.1 Genomic DNA Extraction from Environmental Samples ..............................................31
2.10.2 Genomic DNA Extraction from Pure Cultures ................................................................32 Table of Contents II
2.10.3 Photometrical Quantification of Nucleic Acids.............................................................32
2.10.4 Purification of PCR Products .............................................................................................32
2.10.5 Single Strand Conformation Polymorphism (SSCP) .......................................................32
2.10.5.1 PCR Assays for SSCP....................................................................................................33
2.10.