Bacterial Interactions and Evolution

Group leader: Ákos Kovács

Bacteria rapidly adapt to environment changes and in the presence of other organisms. Our endeavor to understand how bacteria evolve in complex communities facilitates our intention to engineer complex microbiomes and to employ microorganisms in various biotechnological applications. Using Bacillus subtilis, we examine how this bacterium interact during biofilm development with other microorganisms, including both soil-derived bacteria and fungi, and colonise its natural niche, the plant rhizosphere. Experimental evolution is a powerful technique to dissect the adaptation process, but also to prudently improve strains without the need for direct genetic modification.

Our research is focused around the following major topics:

  • chemical ecology of Bacilli
  • interaction in mono- and multi-species biofilms
  • bacteria-plant and bacteria-fungi interaction
  • evolution of microbial interactions

We explore the diversity, function and evolution of secondary metabolite production in the Bacillus genus using a library of isolates, targeted modification of biosynthetic gene clusters, construction of synthetic microbial communities, and bioinformatic analysis of biosynthetic gene clusters. 

Laboratory biofilms present a powerful system to explore the social interaction of microbes. Due to the large population size and rapid generation time, we can easily investigate the conversion of social interaction that enables us to reveal the evolutionary stable strategies. We use the biofilms of B. subtilis to test various predictions from the field of evolutionary theory, including the burdens of public good production, stability of division of labor, evolution of phenotypic heterogeneity, and influence of selection pressure. Further, we use this knowledge to dissect the selective forces in multi-species communities. 

To understand the ecology of Bacilli, we study how B. subtilis evolves to the presence of various organisms, e.g. the black mold fungus, Aspergillus niger, or during colonization of the plant root. Using dedicated selection regimes, we aim to evolve production strains of Bacilli for desired applications in green biotechnology.

Publication highlights:

  (1) Biofilms of Bacilli
- Arnaouteli S, Bamford N, Stanley-Wall N, Kovács ÁT (2021) 
Bacillus subtilis biofilm formation and social interactions. Nature Reviews Microbiology 19(9):600-614
- Martin M, Dragoš A, Otto SB, Schäfer D, Brix S, Maróti G, Kovács ÁT (2020) Cheater-mediated evolution shifts phenotypic heterogeneity in Bacillus subtilis biofilms. ISME Journal 14(9):2302-2312
- Dragoš A, Kiesewalter HT, Martin M, Hsu CY, Hartmann R, Wechsler T, Drescher K, Stanley-Wall N, Kümmerli R, Kovács ÁT (2018) Division of labor during biofilm matrix production. Current Biology 28(12):1903-1913 
- Dragoš A, Martin M, Falcón García C, Kricks L, Pausch P, Heimerl T, Bálint B, Maróti G, Bange G, López D, Lieleg O, Kovács ÁT (2018) Collapse of genetic division of labor and evolution of autonomy in pellicle biofilms. Nature Microbiology 3(12):1451-1460
- Hölscher T, Bartels B, Lin Y-C, Gallegos-Monterrosa R, Price-Whelan A, Kolter R, Dietrich LEP, Kovács ÁT (2015) Motility, chemotaxis and aerotaxis contribute to competitiveness during bacterial pellicle biofilm development. Journal of Molecular Biology 427(23):3695-3708

(2) Secondary Metabolites
- Kiesewalter HT, Lozano-Andrade CN, Wibowo M, Strube ML, Maróti G, Snyder D, Jørgensen TS, Larsen TO, Cooper VS, Weber T, Kovács ÁT (2021) Genomic and chemical diversity of Bacillus subtilis secondary metabolites against plant pathogenic fungi. mSystems 6(1):e00770-20
- Steinke K, Mohite OS, Weber T, Kovács ÁT (2021) Phylogenetic distribution of secondary metabolites in the Bacillus subtilis species complex. mSystems 6(2):e00057-21
- Kiesewalter HT, Lozano-Andrade CN, Strube ML, Kovács ÁT (2020) Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities. Beilstein Journal of Organic Chemistry 16, 2983–2998

(3) Bacillus interaction with plant and microbes
Sun X, Xu Z, Xie J, Thomsen VH, Tan T, Zheng D, Strube ML, Dragos A, Shen Q, Zhang R, Kovács ÁT (2022) Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. ISME Journal 16 (3):774–787
- Lin Y, Alstrup M, Pang JKY, Maróti G, Er-Rafik M, Tourasse N, Okstad OA, Kovács ÁT (2020) Adaptation of Bacillus thuringiensis to plant colonisation affects differentiation and toxicity. mSystems 6(5):e00864-21
- Blake C, Nordgaard M, Maróti G, Kovács ÁT (2021) Diversification of Bacillus subtilis during experimental evolution on Arabidopsis thaliana and the complementarity in root colonization of evolved subpopulations. Environmental Microbiology 23(10):6122-6136
- Blake C, Christensen MN, Kovács ÁT (2021) Molecular aspects of plant growth promotion and protection by Bacillus subtilisMolecular Plant-Microbe Interactions 34(1):15-25


Ákos T. Kovács
DTU Bioengineering
+45 45 25 25 27