Microbiology of the rhizosphere and soil

The diversity of microorganisms in soil is very high in comparison to other ecosystems (Figure 1). The identity of soil inhabiting microorganisms has been intensively studied and information is accumulating about the composition of soil microbial communities, in particular since the application of cultivation-independent molecular methods for the analysis of these communities. Research is driven by the questions how such communities establish and sustain in soil, including the identification of environmental factors that shape microbial communities, and how microorganisms contribute to soil ecosystem functioning. This applies in particular to those organisms that remain uncultured and are thus not available for laboratory in depth studies under controlled conditions.

Figure 1: Rarefaction curves showing the diversity of bacterial communities in different ecosystems. Curves are derived from 16S rRNA gene based clone library analysis. OTU = operational taxonomic unit. © Microbiology of the rhizosphere

Figure 2: Root system of a soybean plant with nodules harboring bacteroids of Bradyrhizobium japonicum, a bacterial genus that is able to fix nitrogen and provide it to the plant in exchange to carbon compounds; a typical example of a symbiotic interaction between microorganisms and plants. © Microbiology of the rhizosphere

Soils provide very heterogeneous habitats for microorganisms. A particular habitat and hot spot of microbial activity is the rhizosphere, that part of the soil that is influenced by plant roots. Compared to the bulk soil, the rhizosphere harbors a distinct, less complex microbial community.

Microorganisms in soil are well known for their role in the mineralization of organic material, a process that delivers nutrients for plants to growth. Moreover, microorganisms are involved in shaping soil architecture and some of them can affect plant growth and development even more directly, e. g. by improving nutrient availability of the plant via a symbiotic lifestyle together with the plant or by plant protection against pathogens (see for example in Figure 2). At the same time, the soil is habitat for plant pathogenic microorganisms. The specific functions of many microbial taxa within a soil or rhizosphere microbial community remain currently unknown, especially for those organisms that cannot readily be cultured in laboratories, which is actually the case for the vast majority of soil inhabiting microorganisms. Thus, linking function to identity is often a challenge and one of the major aims in our soil microbial ecology studies.

Our research is driven by the interest to better understand the cycling of carbon compounds in the rhizosphere and soil. We aim at the identification of microorganisms involved in carbon conversion processes, as well as the factors that influence abundance and activity of these microorganisms. Cultivation-independent molecular methods are applied to analyze microbial communities. Moreover, we study representative bacterial model strains under laboratory conditions to obtain deeper insight into the physiology of specific strains under controlled conditions. Such analyses help to better understand their role in the soil or rhizosphere and to predict the responses of these microorganisms to environmental changes in their natural ecosystems.

Selected publications:

Frindte, K., Pape, R., Werner, K., Löffler, J., Knief, C. (2019) Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients. ISME J. in press

Krause, L., Biesgen, D., Treder, A., Schweizer, S. A., Klumpp, E., Knief, C., Siebers, N. (2019) Initial microaggregate formation: association of microorganisms to montmorillonite-goethite aggregates under wetting and drying cycles. Geoderma. In press

Maarastawi, S. A., Frindte, K., Bodelier, P. L. E., Knief, C. (2019) Rice straw serves as additional carbon source for rhizosphere microorganisms and reduces root exudate consumption. Soil Biol. Biochem. in press

Maarastawi, S. A., Frindte, K., Geer, R., Kröber, E., Knief, C. (2018)
Temporal dynamics and compartment specific rice straw degradation in
bulk soil and the rhizosphere of maize. Soil Biol. Biochem 127: 220-212.

Maarastawi, S. A., Frindte, K., Linnartz, M., Knief, C. (2018) Crop
rotation and straw application impact microbial communities in Italian
and Philippine soils and the rhizosphere of Zea mays. Front. Microbiol.
9: 1295.

Totsche, K. U., Amelung, W., Gerzabek, M. H., Guggenberger, G., Klumpp, E., Knief, C., Lehndorff, E., Mikutta, R., Peth, S., Prechtel, A., Ray,
N., Kögel-Knabner, I. (2018) Microaggregates in soils. J. Plant Nutr.
Soil Sci. 181: 104-136.

Knief, C., Delmotte, N., Chaffron, S., Stark, M., Innerebner, G., Wassmann, R., von Mering, C. Vorholt, J. A. (2012) Metaproteomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6: 1378-1390.

Delmotte, N., Ahrens, C. H., Knief, C., Qeli, E., Koch, M., Fischer, H-M., Vorholt, J. A., Hennecke, H., Pessi, G. (2010) An integrated proteomics and transcriptomics reference dataset provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 10: 1391-1400.