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Bacterial adaptations to nutrient and energy limitationBakterielle Anpassung an Nahrungs- und Energielimitierung

Adaptation of anoxygenic phototrophs to extreme low-light and long-wavelength IR

The Black Sea chemocline represents the largest extant habitat of anoxygenic phototrophic bacteria on Earth and harbours a monospecific population of Chlorobium BS-1. Application of a highly specific RT-qPCR method which targets the internal transcribed spacer (ITS) region of the rrn operon of BS-1 demonstrated that cells at 80 - 95 m water depths are physiologically active at in situ light intensities below 0.18 µmol quanta•m-2•s-1 which renders it the most extreme low-light-adapted phototroph known to date. According to laboratory measurements, Chlorobium BS-1 has a maintenance energy requirement of ~1.6-4.9•10-15 kJ•cell-1•d-1 which is the lowest value determined for any bacterial culture so far. Chlorobium BS-1 thus can serve as a laboratory model to elucidate general cellular mechanisms of long-term starvation survival. Because of its adaptation to extreme low light marine environments, Chlorobium BS-1 also represents a suitable indicator for palaeoceanography studies of deep photic zone anoxia in ancient oceans.

Whole cells of the purple sulfur bacterium strain 970 exhibit an unusual absorption peak at 963 nm. Therefore, the puf operon encoding the light-harvesting complex 1 (LHC1) and the photosynthetic reaction center proteins was amplified, cloned and sequenced. A deletion between αHis0 and αTrp+11, thought to be responsible for the red shifted Qy absorption in Thermochromatium tepidum was also detected in strain 970 and Thiorhodovibrio winogradskyi, whereas αLys+12 is replaced by histidine only in strain 970. Based on our structural modeling, the side chain of this αHis is predicted to be in close proximity to the BChla, suggesting that it exerts a modulating effect on the spectral properties of the highly unusual LHC1 complex of strain 970.

Adaptations of marine bacterioplankton to nutrient limitation and refractory organic carbon substrates

The Eastern Mediterranean Sea represents one of the most oligotrophic habitats on Earth and contains very low concentrations of inorganic nutrients. Organic carbon substrates and phosphate elicit a pronounced chemotactic response of heterotrophic bacterioplankton whereby different copiotrophic members of the bacterioplankton exhibit distinct responses. In particular, the alphaproteobacterium Thalassospira sp. exhibited a pronounced response towards inorganic phosphate. This previously unrecognized component of marine ultraoligotrophic bacterioplankton thus seems to be specifically adapted to accumulate at point sources of phosphate. The present study provides the first evidence for a chemotactic activity of marine bacterioplankton towards phosphate, thereby identifying an alternative strategy of motile bacteria to enhance their phosphate acquisition. The differential chemotactic response has implications for our understanding of the ecological niche of typical but low abundance marine planktonic genera and their potential role in the marine carbon and phosphorus cycles.

Global warming causes a mobilization of terrigenous refractory carbon in arctic Permafrost. The increased input of organic carbon into the neighboring coastal seas is expected to result in considerable changes of the marine carbon cycle. Seasonal variations of terrigenous dissolved organic carbon (tDOC) and increased CO2 emissions in the coastal seas, together with low tDOC in the open ocean suggest an effective mineralization in coastal areas. However, little is known about the microorganisms involved, their physiological properties and environmental factors which control microbial tDOC mineralization in the marine habitats. DSMZ participates in the collaborative project ATKiM (Abbaubarkeit von arktischem terrigenen Kohlenstoff im Meer - Degradation of arctic terrigenous carbon in the sea) that is funded by the Leibniz Association and merges the scientific expertise of four Leibniz-Institutes (DSMZ, IOW, IGB, and MfN) with that of university partners (Rostock, Greifswald, Bremen, Oldenburg, and Stockholm). Within this framework DSMZ studies the activity patterns of bacterioplankton in response to tDOC degradation (using metatranscriptomics), isolate representative members of the bacterioplankton and investigate their physiology.

Adaptations of soil bacteria to nutrient limitation and feedbacks to changes in land use

Exploratories for Functional Biodiversity Research

So far, studies of the functional relevance of bacterial diversity have mostly been limited to a few groups of Proteobacteria involved in the N-cycle and to rhizosphere bacteria. Acidobacteria represent a major group of soil bacteria but their role in biogeochemical cycles is poorly understood. The project ProFIL (Prokaryotic Diversity Changes and their Functional Interrelation to Land Use) is part of the DFG-funded Exploratories for Functional Biodiversity Research.

Using a land use gradient across three long-term research sites (exploratories) as the major variable, we conduct a detailed study of the composition Acidobacteria community, physiological key traits and the functional implications of Acidobacteria diversity. In order to identify the biotic and abiotic determinants of Acidobacteria diversity and activity, deep sequencing of ribosomal RNA genes and quantification of the ribosome content is conducted and correlated with environmental parameters by multivariate statistical analyses. Novel information on the metabolic traits of dominant soil Acidobacteria is obtained by analyses of existing metagenomic libraries and by characterizing representative isolates.

The Future Okavango

This project is part of The Future Okavango which is funded by the BMBF-Research Program “Sustainable Land Management“. We focus on a quantitative understanding of bacterial carbon and nitrogen transformations as major determinants of soil fertility. This will elucidate the feedback mechanisms between different soil management practices and bacterial mineralization, ammonification and nitrification in the Okavango region that comprises parts of Angola, Namibia and Botswana. These processes are central to the nutrient supply and stability of savanna soils and will be analyzed by quantitative models. The bacteria involved in biogeochemical nutrient cycling are identified by molecular techniques. Representative species are isolated by novel cultivation approaches, physiologically characterized, and transferred to cooperating African institutions for future studies of their application potential. In cooperation with other subprojects of TFO, quantitative models of C- and N-cycles in the Okavango savanna soils will be generated. These models will aid in the understanding of soil nutrient supply and in the assessment of future land use scenarios and the impact of predicted changes in local climate.

Representative publications

  • Foesel BU, Nägele V, Naether A, Wüst PK, Weinert J, Bonkowski M et al (2013). Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils. Environmental Microbiology: In press.
  • Foesel, B.U., Rohde, M., Overmann, J. (2013) Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil - the first described species of Acidobacteria subdivision 4. Syst. Appl. Microbiol. 36: 82-89
  • Naether, A., Foesel, B.U., Naegele, V., Wüst, P.K., Weinert, J., Bonkowski, M., Alt, F., Oelmann, Y., Polle, A., Lohaus, G., Gockel, S., Hemp, A., Kalko, E. K. V., Karl Eduard Linsenmair, K.E., Pfeiffer, S., Renner, S., Schöning, I., Weisser, W. W., Wells, K., Fischer, M., Overmann, J., Friedrich, M.W. (2012) Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils. Appl. Environ. Microbiol. 78: 7398-7406.
  • Birkhofer K., Schöning I., Alt F., Herold N., Klarner B., Maraun M., Marhan S., Oelmann Y., Wubet T., Yurkov A., Begerow D., Berner D., Buscot F., Daniel R., Diekötter T., Ehnes R.B., Erdmann G., Fischer C., Foesel B., Groh J., Gutknecht J., Kandeler E., Lang C., Lohaus G., Meyer A., Nacke H., Nähter A., Overmann J., Polle A., Pollierer M.M., Scheu S., Schloter M., Schulze E.-D., Schulze W., Weinert J., Weisser W.W., Wolters V., Schrumpf M. (2012) General relationships between abiotic soil properties and soil biota across spatial scales and different land-use types. PLoS ONE 7: e43292.
  • Sinninghe Damsté J.S., Rijpstra W.I.C., Hopmans E.C., Weijers J.W.H., Foesel B.U., Overmann J., Dedysh, S. (2011) 13,16-Dimethyl octacosanedioic acid (iso-Diabolic Acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. Appl. Environ. Microbiol. 77: 4147-4154.
  • Rücker, O., Köhler, A., Behammer, B., Sichau, K., Overmann, J. (2011) Puf operon sequences and inferred structures of light-harvesting complexes of three closely related Chromatiaceae exhibiting different absorption characteristics. Arch Microbiol. 2012 Feb;194(2):123-34.
  • Hütz, A., Schubert, K., Overmann, J. (2011) Thalassospira sp. isolated from the oligotrophic Eastern Mediterranean Sea exhibits chemotaxis toward inorganic phosphate during starvation. Appl. Environ. Microbiol. 77: 4412–4421.
  • Marschall, E., Jogler, M., Henssge, U., Overmann, J. (2010) Large scale distribution and activity patterns of an extremely low-light adapted population of green sulfur bacteria in the Black Sea. Environ. Microbiol. 12: 1348-1362.
  • Koch, I.H., Gich, F., Dunfield, P.F., Overmann, J. (2008) Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., two novel acidobacteria isolated from alpine and forest soils. Int. J. Syst. Evol. Bacteriol. 58: 1114-1122.
  • Manske, A.K., Henßge, U., Glaeser, J., Overmann, J. (2008) Subfossil 16S rRNA gene sequences of green sulfur bacteria as biomarkers for photic zone anoxia in the ancient Black Sea. Appl. Environ. Microbiol. 74: 624-632
  • Overmann, J. (2005) Chemotaxis and behavioural physiology of not-yet-cultivated microbes. Methods in Enzymology Vol. 397, Chapter II.8, p. 133-147. Elsevier, San Diego, USA
  • Coolen, M.J.L., Cypionka, H., Smock, A., Sass, H., Overmann, J. (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296, 2407-2410.
Photo of Jörg  Overmann
Prof. Dr. Overmann, Jörg
Phone: +49-531/2616-352

Scientific Director / Wissenschaftlicher Direktor

Photo of Wiebke  Behrens
Dr. Behrens, Wiebke
Phone: +49-531/2616-323
Photo of Selma  Gomes Vieira
Gomes Vieira, Selma
Phone: +49-531/2616-364
Photo of Katharina  Huber
Dr. Huber, Katharina
Phone: +49-531/2616-365

Corynebacterineae, Pseudonocardineae, Rhodobacteraceae, Acidobacteria, Elusimicrobia