Environmental determinants of biopolymer degraders in agricultural soils

Principle investigators: PD Dr. S. Kolb and Prof. Dr. H.L. Drake

Co-worker: A. Wieczorek

Background:
The structural polysaccharides cellulose and chitin of plants, fungi, and arthropods are major components of fresh organic matter in agricultural soils. These biopolymers are carbon sources of soil microbial communities linked to soil redox processes. Soil aggregates of water-unsaturated soil form natural boundaries of oxic conditions outside and oxygen-limited conditions inside. These biogeochemical interfaces lead to a highly heterogeneous oxygen distribution on a millimetre scale. The effects and mechanisms of the toxicity of herbicides on biopolymer degrading communities in such highly compartmentalized soils have not been resolved. The preceding project resolved phylogenetic identities of known and novel prokaryotes linked to cellulose degradation under both oxic and anoxic conditions, and demonstrated that the acidic herbicides bentazone and MCPA impair microbial processes involved in cellulose degradation. The project of the SPP1315 second funding period will (I) identify chitin-degrading prokaryotes, fungi, and protists that are active in oxic and anoxic microzones, (II) determine the tolerance of various cellulolytic and chitinolytic taxa to bentazone and MCPA, (III) characterize key chitin-degraders, and (IV) will quantitatively assess oxygen distribution during biopolymer degradation in an agricultural soil.

Objectives:
1. Identification of cellulose and chitin degrading Prokaryotes, Fungi, and protists in the model agricultural soil from Klostergut Scheyern.
2. Isolation of chitin-degrading microbes.
3. Visualization and quantification of activity hotspots of biopolymer degraders in soil cross sections.

Methods:
Molecular (stable isotope probing [SIP], quantitative PCR, Pyrosequencing), chemical (gas chromatography [GC], high performance liquid chromatography [HPLC] for arganic substrates products, Bentazon, MCPA); 2D UV imaging of oxygen, redox potential (with S. Oswald, Potsdam) in soil cross section

Cooperation within the SPP 1315:
Prof. Dr. S.E. Oswald (Univ. Potsdam), Dr. A. Chatzinotas (UFZ Leipzig), Prof. Dr. M. Schloter (TU Munich) and Prof.Dr.  J.C. Munch (TU Munich)