From culture to community: the physiology, regulation and community functions of alginate degradation by marine Gammaproteobacteria and Bacteroidetes

• Applicant: Dr. Matthias Wietz
• Subject Area: Microbial Ecology and Applied Microbiology ; Metabolism, Biochemistry and Genetics of Microorganisms
• Term: from 2012 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 212985721

• Final Report Year: 2019

Final Report Abstract

The project has illuminated cellular, community and ocean-wide aspects of marine bacterial polysaccharide degradation, including molecular studies of environmental microbiota and eco-physiological-genomic analyses of isolated model strains. Five published and four almost complete manuscripts provide comprehensive insights into bacterial community dynamics, physiology, gene content and regulation, ecological strategies, interactions, and metabolite production associated with bacterial polysaccharide degradation. The combination of culture-based and environmental studies resulted in fundamental understanding of individual bacterial capacities and how these translate to the broader ecological context. The project has met the major proposed aims, answering most major points and hypotheses in both funding phases: first holistic investigation of cellular processes during polysaccharide degradation by transcriptomics, proteomics and exometabolomics in different growth phases; polysaccharide particles as microhabitats; the community aspect of alginate degradation; succession of hydrolytic populations during polysaccharide degradation; "Bacteroidetes" biogeography; and interactions of strains with varying physiological potentials. The investigated processes on particles are immensely relevant in view of surface-benthos coupling and nutrient microhabitats [27-29], and our analyses of algal polysaccharide particles are excellent addition to other work on chitin particles [30]. The established collaborations were highly productive and lay essential groundwork for future studies, for instance regarding fine-scale connections between bacterial growth and certain polysaccharides through meta-omics and carbohydrate microarrays. Change of plans mainly included an increased focus on "Gammaproteobacteria" following results from phase 1-1, providing important knowledge on so-far understudied players in marine polysaccharide degradation. Furthermore, the focus of phase 1-2 was extended to other important polysaccharides (pectin, laminarin) including co-incubation of different polysaccharides, which maximized the scientific output beyond the original project aims. As opposed to the original proposal, Gene-FISH was not used to identify functional traits in natural bacterial communities, but was ideally replaced by meta-omics thanks to additional funding. Also, time constraints restricted exhaustive co-cultivation of bacteria with different hydrolytic potentials, but the developed RT-qPCR based on strain-specific genes represents an important outlook in this direction. The envisioned collaboration with Prof. Stocker (ETH Zurich) could not be realized, as essential preliminary work (fluorescent labeling of A. macleodii 83-1 for live microscopic imaging) failed despite careful attempts in an extended student project. Finally, it can be stated that economic usage or patenting of results is not envisioned, as the project focused on fundamental ecological aspects of polysaccharide degradation. Nonetheless, the project has promising outlook for future studies, based on the establishment of several hydrolytic model organisms and development of novel experimental systems such as particle experiments, which can be easily reproduced or extended under different viewpoints (e.g. during phytoplankton blooms). In conclusion, the project has succeeded to answer fundamental questions while opening important future perspectives regarding bacterial polysaccharide degradation in the oceans.

Publications

• (2015). Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ. Microbiol. 17:3822–3831
  Wietz, Matthias; Wemheuer, Bernd; Simon, Heike; Giebel, Helge‐Ansgar; Seibt, Maren A.; Daniel, Rolf; Brinkhoff, Thorsten & Simon, Meinhard
  
• (2015). Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ. Microbiol. 17:3857–3868
  Neumann, Anna M.; Balmonte, John P.; Berger, Martine; Giebel, Helge‐Ansgar; Arnosti, Carol; Voget, Sonja; Simon, Meinhard; Brinkhoff, Thorsten & Wietz, Matthias
  
• (2016). Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain. Environ. Microbiol. 18:4369–4377
  Mitulla, Maximilian; Dinasquet, Julie; Guillemette, Ryan; Simon, Meinhard; Azam, Farooq & Wietz, Matthias
  
• (2018). Distinct biogeographic patterns of bacterioplankton composition and single-cell activity between the subtropics and Antarctica. Environ. Microbiol. 20:3100–3108
  Bakenhus, Insa; Dlugosch, Leon; Giebel, Helge‐Ansgar; Beardsley, Christine; Simon, Meinhard & Wietz, Matthias
  
• (2019) Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. The ISME journal 13 (1) 92–103
  Koch, Hanna; Dürwald, Alexandra; Schweder, Thomas; Noriega-Ortega, Beatriz; Vidal-Melgosa, Silvia; Hehemann, Jan-Hendrik; Dittmar, Thorsten; Freese, Heike M; Becher, Dörte; Simon, Meinhard & Wietz, Matthias