751-5123-00L  Rhizosphere Ecology

SemesterAutumn Semester 2016
LecturersH. A. Gamper, T. I. McLaren
Periodicityyearly recurring course
Language of instructionEnglish
CommentNumber of participants limited to 18.

Prerequisites: Only students who have passed the courses 751-3401-00L Pflanzenernährung I and 751-3402-00L Pflanzenernährung II - Integriertes Nährstoffmanagement can be admitted to this course.


AbstractThis course is about the physical, chemical, and biological processes in the rhizosphere and their effect on plant growth. Effects of fertilisers, companion plants, and microbial symbionts, and other microbes on nutrient cycling and plant uptake are discussed. An "intercropping" experiment in the glasshouse is used as a model to check for rhizosphere effects on plant growth and mineral nutrition.
ObjectiveTo gain a holistic understanding of resource-driven and regulatory processes in agricultural and natural ecosystems.
Develop skills on the critical analysis of scientific papers.
Define explanatory hypotheses, identify knowledge gaps for further investigations.
Carry out a multi-disciplinary experiment that involves aspects of soil, (micro-)biology, plant physiology, pathology, and ecology.
Develop manual skills in the set up of a glasshouse experiment, in soil and plant analyses, and in isolation and DNA-based characterisation of rhizobia.
Gain insights on basic methods to analyse (bio-)chemical, molecular genetic, and graphical data.
Discuss and interpret data in the context of the literature.
Prepare a research report in the format of a scientific paper and a poster in the format of a conference paper, partially alone and partially in small groups, using data obtained from the glasshouse experiment.
ContentThis course is designed to stimulate thinking and promote critical analysis of important processes that occur in the rhizosphere. As part of this course, the knowledge acquired will be used for analysing and interpreting experimental data, as well as, preparing a scientific report and conference-type poster.

The course will cover the relative importance of spatial scales and various physicochemical and microbiological dynamics as influenced by roots. We will discuss root traits and activities that influence the immediately root-surrounding soil and thereby contribute to mineral nutrient mobilization and immobilization. An overview of the most relevant root-microbe symbioses for agroecosystems will be provided and root and microbial traits discussed, which could be of use in efforts towards utilization of intercropping and bioinoculants as a possible means of reducing energetically expensive inputs to farming systems. A special emphasis will be given to the importance of physicochemical features of soils and the chemical forms (= species) of elements important for plant uptake.

Practical experience will be gained with setting up a glasshouse experiment, soil and root sampling, basic soil and plant analyses, isolation of rhizobia, determination of the number of colony forming units (CFU), assays to screen for phosphorus and zinc solubilizing bacteria, DNA extraction, PCR amplification, and restriction fragment length polymorphism analysis (RFLP) of host range determining symbiosis-specific genes.

In short, the processes dealt with in this course occur on a small-scale and are generally (bio)chemical and microbiological in nature. Furthermore, they are generally not taken into account using current methods of agronomic management for plant production. However, they are increasingly being recognized as a potentially useful means of obtaining a resource-efficient and hence, economically and environmentally sustainable agricultural system, including for ecosystem restoration. Therefore, the course will invite for critical reflections and exemplify challenges in translating knowledge from scientific studies and ecology into application for plant production.
Lecture notesFor documentation, lecture slides and laboratory protocols will continuously be uploaded to the directory '751-5123-00L Rhizosphere Ecology' on the electronic document exchange platform ILIAS, LDA-ELBA:
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LiteratureYork LM, Carminati A, Mooney SJ, Ritz K, Bennett MJ (2016) The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots. Journal of Experimental Botany, doi: 10.1093/jxb/erw108.

Lynch, James M; and de Leij, Frans (May 2012) Rhizosphere. In: eLS. John Wiley & Sons, Ltd: Chichester.
DOI: 10.1002/9780470015902.a0000403.pub2 http://www.els.net/WileyCDA/ElsArticle/refId-a0000403.html

Kuzyakov Y, Blagodatskaya E. (2015) Microbial hotspots and hot moments in soil: Concept and review. Soil Biology and Biochemistry 83: 184-199.

Cardon, CG, Whitbeck, JL (Eds) (2007) The rhizospere: An ecological perspective, Academic Press, pp. 232, ISBN: 978-0-12-088775-0 http://www.sciencedirect.com/science/book/9780120887750

White PJ, George TS, Dupuy LX, Karley AJ, Valentine TA, Wiesel L, Wishart J. (2013) Root traits for infertile soils. Frontiers in Plant Science 4, doi: 10.3389/fpls.2013.00193.

Neumann G, George TS, Plassard C (2009) Strategies and methods for studying the rhizosphere - the plant science toolbox. Plant and Soil 321: 431-456.

Morgan, J. B. & Connolly, E. L. (2013) Plant-soil interactions: Nutrient uptake. Nature Education Knowledge 4(8):2 Link

Pinton, R., Varanini, Z., Nannipieri, P. (2007) The rhizosphere: Biochemistry and organic substances at the soil-plant interface, Taylor & Francis, London, UK, pp. 472 http://www.crcnetbase.com/isbn/978-0-8493-3855-7

Hinsinger, P., Bengough, A. G., Vetterlein, D., Young, I. M. (2009): Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant and Soil 321, 117-152.

Beeckman, T. (Ed) (2013) Plant roots: The hidden half, 4th ed., CRC Press, Taylor & Francis Group, London, UK, pp. 848 http://www.crcnetbase.com/doi/book/10.1201/b14550

van der Heijden, Sanders (Eds) (2002) Mycorrhizal ecology, Ecological Studies 157, Springer, Berlin, pp. 469, ISCBN 978-3-540-00204-8 http://www.springer.com/life+sciences/ecology/book/978-3-540-00204-8

Kuzyakov Y, Xu X. (2013) Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance. New Phytologist 198: 656-669.

Hinsinger, P., Betencourt, E., Bernard, L., Brauman, A., Plassard, C., Shen, J. B., Tang, X. Y., Zhang, F. S. (2011) P for two, sharing a scarce resource: Soil phosphorus acquisition in the rhizosphere of intercropped species. Plant Physiology 156, 1078-1086.

Bender SF, Wagg C, van der Heijden MGA (2016) An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends in Ecology & Evolution. doi: 10.1016/j.tree.2016.02.016.

Withers PJA, Sylvester-Bradley R, Jones DL, Healey JR, Talboys PJ. (2014) Feed the crop not the soil: rethinking phosphorus management in the food chain. Environmental Science & Technology 8: 6523-6530.

How microbes can feed the world (American Academy of Microbiology) Link

Can microbes feed the world? (Society for general microbiology) Link

Popular science entries to the significance of processes in the rhizosphere:
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http://nautil.us/issue/34/adaptation/junk-food-is-bad-for-plants-too

Ecological understanding (Second Edition)
The nature of theory and the theory of nature http://www.sciencedirect.com/science/book/9780125545228
Prerequisites / NoticeWe ask all course attendees of the agricultural sciences to have passed the exams at the end of the lectures Plant Nutrition I and II (Nutrient cycling in agroecosystems) by Prof. E. Frossard. All others, have to have successfully worked through the e-learning module Plant Nutrition I by Prof. E. Frossard:
https://moodle-app2.let.ethz.ch/course/view.php?id=279
Remark: The course is designed to be complementary to those on Radioisotopes in Plant Nutrition (751-3405-00L), and Nutrient Fluxes in Soil-Plant Systems (751-3404-00L), although some thematic overlaps cannot be avoided. Special emphasis is given to plant-microbe-soil interactions and an appreciation of whole plant functioning in the ecological context. You will familiarize yourself with bacterial isolation, cultivation, enumeration, as well as, molecular detection, discrimination and identification techniques for rhizosphere and root-associated microbes.
Marking will consider the efforts and outcome of work by the individual participant as well as results of work in small groups. Activities for the course will result in posters and reports in the format of a conference and scientific paper. Reports will be due on Friday January 6, 2017.
Maximum number of participants: 18 (Attention: Admission will be on a first come first served basis - inscribe early!).
Students of D-USYS will be reimbursed via bank transfer for train and bus tickets of the zones 121 and 122 (Please send all tickets with the bank details to Christiane Gujan (Link).