Gram-negative Bacteria

PI: Dr. Richard Hahnke

Increasing costs for petroleum and agricultural food products have put attention on straw, trees, nonfood crops, and other low-cost agricultural waste materials as alternative, second generation resources. The transformation of plant and algal biomass into saccharides requires the separation and depolymerization of cellulose, hemicellulose and lignin. These saccharides can be used for production of building-block chemicals (such as ethanol) by fermentation or transformation (enzymatically or chemically). However, the high amount of cellulose and hemicellulose in corn straw, woody and herbaceous crops remains a key challenge for their efficient and cost-effective depolymerization. In biorefineries, lignocellulose is pretreated using chemical and physical procedures to make the biomass matrix more accessible to enzymes. As a sustainable alternative, microorganisms or microbial communities can assist either in the decomposition or directly decompose and transform plant and algae derived polysaccharides.

We investigate microbial communities decomposing straw in natural continuous cultures, e.g. in graduation tower packed with straw. Our aim is to enrich and isolate cellulose decomposing microorganisms and screen them for their potential to decompose plant and algae derived biomass. Furthermore, we screen genomes of type strains (I) to predict their polysaccharide decomposition potential indicated by the number and diversity of genes encoding for carbohydrate active enzymes (CAZyme) and (II) to gain further insights into whether strains from different ecological habitats possess distinct biochemical pathways and sets of CAZymes. Motivated by their great potential for biotechnological applications, we have focused on type strains of the families Flavobacteriaceae, Alteromonadaceae (Bacteria) and Natrialbaceae (Archaea).

This is a joint research project with the group of Halophilic and Phototrophic Bacteria.

Selected Publications

1. Panschin, I., Becher, M., Verbarg, S., Spröer, C., Rohde, M., Schüler, M., Amann, R.I., Harder, J., Tindall, B.J., Hahnke, R.L. (2017) Description of Gramella forsetii sp. nov., a marine Flavobacteriaceaeisolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al.2011. Int J Syst Evol Microbiol67: 697-703.
2. Panschin, I., Huang, S., Meier-Kolthoff, J.P., Tindall, B.J., Rohde, M., Verbarg, S., Lapidus, A., Han, J., Trong, S., Haynes, M., Reddy, T.B.K., Huntemann, M., Pati, A., Ivanova, N.N., Mavromatis, K., Markowitz, V., Woyke, T., Göker, M., Klenk, H.-P., Kyrpides, N.C., Hahnke, R.L. (2016) Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050^T(DSM 19838^T) and Gramella portivictoriae UST040801-001^T(DSM 23547^T), and emended description of Gramella echinicola Nedashkovskayaet al.2005. Gramella portivictoriae Lau et al.2005. Stand Genomic Sci 11: 1-16.
3. Tashkandy, N., Sabban, S., Fakieh, M., Meier-Kolthoff, J.P., Huang, S., Tindall, B.J., Rohde, M., Baeshen, M.N., Baeshen, N.A., Lapidus, A., Copeland, A., Pillay, M., Reddy, T.B.K., Huntemann, M., Pati, A., Ivanova, N., Markowitz, V., Woyke, T., Göker, M., Klenk, H.-P., Kyrpides, N.C., Hahnke, R.L. (2016) High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707^T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5^T. Stand Genomic Sci 11: 11-42.