Prof. Dr. Matthias Noll

Research areas
  • Environmental microbiology – Molecular microbial ecology
  • Material resistance against microorganisms
  • Antimicrobial substances, Antibiotics / Biocides / essential oils und countermeasures to biofilms and biofilm formation

  • Food microbiology
  • Bioanalysis
Teaching areas
  • General Biology
  • Microbiology
  • Molecular biological analysis

Phone: +49 (0)9561 317-645
Fax: +49 (0)9561 317-346
Room 2-215
e-Mail: matthias.noll[at]

Prof. Noll has expertise in microbial ecology, environmental and food microbiology.

Current Projects

The effect of forest management intensity, tree species and fungal-bacterial diversity on resource use, decomposition and gas emissions in dead Wood Funwood IV (funding by German science foundation,

Wood-decomposition in forest ecosystems is a very important process with immense ecological consequences. Dead wood is an important structural component of forest ecosystems and it influences a large number of ecosystem functions of which the most relevant are C sequestration, nutrient cycling, and habitat provision for wood dwelling organisms. FunWood IV project will focus on ecosystem functions in dead wood decomposition and corresponding biodiversity. It aims to test experimentally whether increasing species richness will result in higher functional diversity in dead wood decomposer communities, and how the decomposer diversity and ecosystem processes are influenced by forest management intensity. FunWood IV will combine a range of state-of-the-art techniques (amplicon gene sequencing, metaproteomics, protein-SIP, CO2 emission rate and C/N content analyses with its isotopic signature) to provide an improved understanding on how decomposer communities execute wood degradation processes under fluctuating temperatures. Results will be correlated with existing and new formed data sets to improve our understanding of ecosystem functioning in microbial dead wood decomposition. Moreover, the effect of forest management and tree species effect on the dead wood decomposition rates across geographic dimensions will be analyzed. 

New combinations of food additives with anti-fungal and anti-yeast effects (funded by Adalbert-Raps-Stiftung)

Ascomycetes, yeasts and bacteria are known as spoilage microorganisms in food and they are able to change color, texture, taste and smell of food. Moreover, the microbial biomass in food can increase and microbial compounds with health hazard such as mycotoxins can be formed. To prevent food spoilage and presence of pathogenic microorganisms, food additives such as essential oils are used. So far, few knowledge is present of plant compounds that are simultaneously active against ascomycetes, yeasts and bacteria. In this project public databases will be screened to find natural plant compounds with antimicrobial properties. Thereafter, interesting plant compounds will be tested in their antimicrobial activity against relevant spoilage microorganisms in a lab approach. In best case, compounds will be identified with a high antimicrobial activity against a broad range of spoilage microorganisms at low concentration. 

Characterization and use of microbial communities in industrial algae cultures (Cooperation with the University of Hochschule Anhalt)

The industrial production of manifold substances from microalgal cultures is typically stable, but frequently contaminations by intracellular zoosporic fungal parasites like Aphelida are causing production loss. While contamination management is mainly based on fungicides, an alternative approach to circumvent infections is the support of indigenous microbial communities of microalgae cultures. 

The aim of this work was to investigate aphelid infection patterns on monocultures of seven microalgae species commonly used in biotechnology. Microbial communities of microalgal cultures were retrieved from axenic or open industrial microalgae settings. Aphelida were more effective to infect species that were phylogenetically closely related to the main host Scenedesmus vacuolatus. All members of the family Scenedesmaceae showed typical Aphelida infection pattern such as a clear decrease in growth rate, cell density, chlorophyll absorbance and destruction of cell structures through intracellular phagocytosis in varying degree of expression. However, members of distantly related microalgal families were unharmed. Independent from host species, presence of microbial communities derived from open settings had a considerable impact on the development of the aphelid infection. In conclusion, results indicate that complex microalgal, bacterial and fungal community compositions are affecting the patterns of aphelid infection. Findings will help to achieve a more stable microalgal production in industrial photobioreactors.   

Characterization of the microbiomon human pathogen ticks and optimization of diagnostic tools for tick associated pathogens (Funding „Bayerisches Staatsministerium für Wissenschaft und Kunst“)

Ticks are known as vectors for severe diseases as Lyme borreliose or TBEV (tick-born encephalitis virus). Also, there is a high probability that ticks carry much more pathogens. Therefore, patients bitten by a tick need fast and precise diagnostic.

This project deals with the characterization of the microbiom on ticks including potential human pathogens. The possibility to transfer diseases should be evaluated statistically valid and explorative. This includes isolation of total DNA and RNA from ticks. Furthermore, species identification and bacterial, viral and eukaryotic diversity inside ticks should be determined by molecular biological methods.

All this should lead to a diagnostic assay, which is able to identify the majority of known and previous unknown pathogens on ticks in Germany, too. This results in a better assessment of disease risk.

Linking deadwood decay and nitrogen cycling: diversity and function of diazotrophs (funded by German Research foundation

The German Research foundation (DFG) granted “Woodstock” (a follow-up project of “Funwood IV” in our research group) in the context of the Biodiversity Exploratories. “Woodstock” addresses the influence of nitrogen-fixing microorganisms (so-called diazotrophs) on the decomposition of deadwood in the forest ecosystem. It is assumed that the input of nitrogen into deadwood by diazotrophs is an important driver of its decay rate. For this reason, the project in collaboration with the University of Bayreuth (Chair of Soil Ecology, Prof. W. Broken) investigates the relationships between quantity, activity and diversity of diazotrophs and the decomposition of dead wood of 13 different tree species under the influence of different forest management intensities.

The project uses current methods to determine the functional diversity of diazotrophs in deadwood such as amplicon sequencing and quantitative PCR as well as analytical methods for C/N elemental analysis and CO2 emission and N2 fixation rate determination.

Ecotoxicological Testing of Biocidal Building Materials by conventional und systems biology approaches (funded by the Bavarian State Ministry of the Environment and Consumer Protection)

Soil ecosystems are exposed to a broad range of toxic compounds, among those various biocides. Building materials are vital source for soil contamination. About 25 % of the annual produced biocides are used in building materials. Biocides are utilized to protect the building materials against animal pests, algae, fungi and other microorganisms. Especially temporal and spatial input of biocidal building materials may heavily charge soils.

In the course of the project representative test samples of building materials as well as component mixtures are incubated in a weathering tester. The ecotoxicity of the gained eluates from the weathering tester was determined by use of established and certificated aquatic and terrestrial ecotoxicological tests. In Addition to the established ecotoxicological testing new only in academic context used High-Throughput Methods, such as proteomics, microbiome analysis and overly sensitive biocide analytics, will be used for soil analysis in cooperation with the research group of Prof. Kalkhof. These new Methods shall improve the ecotoxicological valuation of building materials and therefore increase the environmental safety. In cooperation with the German Environment Agency the used “omics”-methods are to be transferred into standard operating procedures.

Completed Projects

Long-time exposure of bacteria to microbiocides (funding by German Federal Institute of Risk Assessment)

Microbiocides at sublethal concentrations cause an adaption of pathogenic bacteria. In this adaptation process the induction of increased micro-biocides resistances as well as of acquired antimicrobial susceptibility are of major interest in this project. The effect of single disinfections compounds, which were routinely applied for consumer goods and products, on bacterial tolerance and resistance will be tested. The application of micro-biocides shifts a majority of bacteria from a culturable state to a viable but non-culturable state (VBNC). Pathogenic bacteria in VBNC may maintain or reactivate their potential of infectivity by shifts of environmental conditions. VBNC has been described as survival strategy to overcome the effect of micro-biocides. Micro-biocide tolerant Sub-populations may act as source of recurring infections in clinical setup as well as in products and food environments. As VBNC cannot be detected by cultivation-based approaches, these sub-populations will not be detected by such classical approaches. In this project, we are assessing bacteria in the VBNC by molecular biological, microscopic and proteomic analyses to get a better understanding of the induction and bacterial characteristics of VBNC bacteria.

Nisin as food additive in cheese products (funded by the Central Innovation Programme for SMEs by the German Ministry for Economics Affairs and Energy)

Consumption of food spoiled by Listeria monocytogenes can lead to severe diseases or even to death. In former outbreaks, consumption of cheese products such as soft cheese were the source of infection. The lantibiotic nisin is an approved food additive to protect food from spoilage microorganisms such as L. monocytogenes. In this project, a procedure will be developed for soft cheese production to capsulate the nisin. Encapsulation of nisin will enable a delayed release and, therefore, high concentrations of nisin will be bio-available during the cheese production and maturing. As result, an increased food safety will be achieved to enable a better consumer protection. 

Energetic use of organic waste and other agricultural sources (funding by Bavarian Science Foundation)

The project from team Noll is a part of the consortium FOR 10´000 consisting of many companies and universities. The target of FOR 10´000 is the development of a holistic approach to gain energy from organic waste on a municipal level and to extend the expertise of small and medium sized biogas plants. The multi-disciplinary approach will focus on modules for substrate preparation, biogas cleaning to bio-methane, optimized usage of heat, microbial fuel cells, concepts for fermentation residues and excess waters. The group of Prof. Noll will carry out population analyses of biogas and sewage treatment plants and the characterization of the phylogenetic and functional state of the present microbial communities. 

Contract Research (Industrial partners)

Our group has expertise in the analyses of the composition and quantity of complex microbial communities like human skin or faces microbiome (projects funded by industry are running). In addition, attachment and biofilm formation on many surfaces with and without biocide addition/coating were carried out in our group. The growth and adherence of microorganisms on surface can be measured. The effectiveness of biocides to protect material surfaces can be analyzed according to ISO 22196:2007 and other protocols. Bioavailability of biocide after migration has be done for various microorganisms of the safety level 1 and 2.

Migration of biocides from the material can also be assessed as described by Ramos, et al. 2011. 

Ramos M, Jiménez A, Peltzer M, and Garrigós MC. 2012. Characterization and antimicrobial activity studies of polypropylene films with carvacrol and thymol for active packaging. Journal of Food Engineering 109(3):513–519.

ISO22196:2007Plastics — Measurement of antibacterial activity on plastics surfaces.

JISZ 2801:2010Antimicrobial products — Test for antimicrobial activity and efficacy.

ISO22196:2011Measurement of antibacterial activity on plastics and other non-porous surfaces.

Extraction and purification of microorganisms from complex sample matrices (e.g. soil, stool) by means of density gradient centrifugation.

Quantification of total bacteria cell count as well as differentiation of membrane integrity after staining with SYBR/PI.


Roedel, A., Dieckmann, R., Makarewicz, O., Hartung, A., Noll, M., Al Dahouk, S. and Vincze, S. (2020) Evaluation of a vacuum-dried microtiter plate for rapid biocide susceptibility testing of clinical Enterococcus faecium isolates. MDPI Microorganisms 8 (4):551.

Kipping, L., Holzscheck, N., Maurer, F., Muszynski, S., Noll, M. and Jehmlich, N. (2020) Microbial metaproteome data from decayed beech dead wood. Data in Brief 29:105285.

Noll, M., Trunzer, K., Vondran, A., Vincze, S., Dieckmann, R., Al Dahouk, S. and Gold, C. (2020) Benzalkonium chloride induces a VBNC state in Listeria monocytogenes. MDPI Microorganisms 8 (2):184.

Haange, S.-B., Jehmlich, N., Hintschich, C., Hankir, M., Wehrmann, D., Seyfried, F., Froment, J., Hübschmann, T., Müller, S., Wissenbach, D., Kang, S., Büttner, C., Panagiotou, G., Noll, M., Rolle-Kampczyk, U., Fenke, W. and von Bergen, M. (2020) Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. Microbiome 8:13.

Purahong, W., Sadubsarn, D., Tanunchai, B, Wahdan, S. F. M., Sansupa, C., Noll, M., Paatsch, T., Wu, Y.-T., Buscot, F. (2019) First insights into the mangrove tree microbiome reveal significant differences in taxonomic and functional composition among plant and soil compartments. MDPI Microorganisms 7 (12):585.

Noll, M. (2019) Optimierung in der Zecken-Diagnostik. Laborpraxis November:14-15.

Buettner, C., Jehmlich, N., von Bergen, M. and Noll, M. (2019) Pseudomonas spp. are key players in agricultural biogas substrate degradation. Scientific Reports 9:12871.

Rödel, A., Dieckmann, R., Brendebach, H., Hammerl, J. A., Kleta, S., Noll, M., Al Dahouk S. and Vincze, S. (2019) Biocide tolerant Listeria monocytogenes isolates from German food production plants do not show cross-resistance to clinically relevant antibiotics. Applied Environmental Microbiology: 85:e01253-19.

Szendy, M., Kalkhof, S., Bittrich, S. Kaiser, F., Leberecht, C., Labudde, D., and Noll, M. (2019) Structural change in GadD2 of Listeria monocytogenes field isolates supports nisin resistance. International Journal of Food Microbiology 305: 108240-108246.

Noll, M., Büttner, C. and Lasota, S. (2019) Copper containing wood preservatives shifted bacterial and fungal community compositions in pine sapwood in two field sites. International Biodeterioration and Biodegradation 142:26-35.   

Jansen, W., Lind, C., Noll, M., Nöckler, C. and Al Dahouk S. (2019) Brucella-positive raw milk cheese sold on the inner European market: a public health threat due to illegal import? Food Control 100:130-137.

Szendy, M., Westhäuser, F., Baude, B., Reim, J., Dähne, L. and Noll, M. (2019) Controlled release of nisin from Neusilin particles to enhance food safety of sour curd cheese. Journal of Food Science and Technology 56:1613-1621.

Lasota, S., Stephan, I., Horn, M. A., Otto, W. and Noll, M. (2019) Copper in wood preservatives delayed wood decomposition and shifted soil fungal but not bacterial community composition. Applied and Environmental Microbiology 85: e02391-18.

Buettner, C. and Noll, M. (2018) Comparing microbial community compositions of biogas and sewage treatment plants by analyzing 16S rRNA gene data. Data in Brief 21:395-402.

Westhäuser, F. and Noll, M. (2018) Ätherische Öle wirken natürlich antimikrobiell. DEI Lebensmittel Produktion Verpackung Food Design 7-8:30-31.

Buettner, C. and Noll, M. (2018) Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants. International Biodeterioration and Biodegradation 133:124-132.

Noll, M., Kleta, S. and Al Dahouk S. (2018) Antibiotic susceptibility of 259 Listeria monocytogenes strains isolated from food, food-processing plants and human samples in Germany. Journal of Infection and Public Health 11: 572-577.

Schmalenberger, A. and Noll, M. (2014) Bacterial communities in grassland turfs respond to sulphonate addition while fungal communities remain largely unchanged. European Journal of Soil Biology 61:12-19.

Conrad, R., Ji, Y., Noll, M., Klose, M., Claus, P. and Enrich-Prast, A. (2014) Response of the methanogenic microbial communities in Amazonian oxbow lake sediments to desiccation stress. Environmental Microbiology 16:1682-1694.

Weiler, C., Ifland, A., Naumann, A., Kleta, S. and Noll M. (2013)
Incorporation of Listeria monocytogenes strains in raw milk biofilms. International Journal of Food Microbiology 163:61-68.

Naumann, A., Stephan, I. and Noll M. (2012) Material resistance of weathered wood-plastic composites against fungal decay Biodeterioration and Biodegradation 75:28-35.

Jakobs-Schönwandt, D., Mathies, Abraham, W.-R., H., Pritzkow, W., Stephan, I. and Noll, M. (2010) Biodegradation of a biocide (Cu-Cyclohexyldiazenium Dioxide) component of a wood preservative by a defined soil bacterial community. Applied and Environmental Microbiology 76: 8076-8083.

Noll, M., Frenzel, P. and Conrad, R. (2008) Selective stimulation of type I methanotrophs in a rice paddy by urea fertilisation revealed by stable isotope probing. FEMS Microbiology Ecology 65: 125-132.

Conrad, R., Klose, M., Noll, M., Kemnitz, D. and Bodelier, P. (2008)
Effect of cultivar and soil type on composition and activity of the methanogenic archaeal community inhabiting rice roots. Global Change Biology 14: 657-669.

Noll, M., Matthies, D., Frenzel, P., Derakshani, M. and Liesack, W. (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environmental Microbiology 7: 382-395.

Aktuelle Publikationsliste:


Alice Rödel

externe Doktorandin, Bundesinstitut für Risikobewertung