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Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities

The ISME Journal volume 17, pages 2014–2022 (2023)Cite this article

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Abstract

Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150–500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.

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Fig. 1: Initial hypothesis of carbon fluxes and mechanisms shaping lenticular biofilm morphology.
Fig. 2: Representativeness of isolates from fermentative granular biofilms.
Fig. 3: FISH micrographs of fermentative granular biofilms.
Fig. 4: Spatial organization of key members of granular biofilms.
Fig. 5: Single-cell anabolic activity across transects within disc-shaped biofilms.
Fig. 6: Anabolic activity response to lactic acid amendment per taxonomic group and per transect.
Fig. 7: Revised, observation-based hypothesis of carbon fluxes and mechanisms of lenticular biofilm morphology.

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Data availability

16S rRNA gene sequences have been deposited to NCBI GenBank under accession numbers OP799682–OP799726.

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Acknowledgements

PC was supported by UGent Special Research Fund (BOF15/DOC/286) and the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research (#DE-SC0020356). RG is supported by the Special Research Fund of Ghent University (grant number BOF19/STA/044). GLC and VJO were supported by grants from the Department of Energy, Office of Science, Office of Biological and Environmental Research (#DE-SC0020373). VJO was also supported by the Life Sciences-Simons Collaboration on Principles of Microbial Ecosystems (PriME) Program from the Simons Foundation (Award 542393).

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Authors and Affiliations

  1. Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium

    Pieter Candry, José Maria Caravajal-Arroyo, Tim Lacoere, Ramon Ganigué & Korneel Rabaey

  2. Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA

    Pieter Candry & Mari-Karoliina Henriikka Winkler

  3. Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA

    Grayson L. Chadwick & Victoria J. Orphan

  4. Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium

    Ramon Ganigué & Korneel Rabaey

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  1. Pieter Candry
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  2. Grayson L. Chadwick
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Contributions

Conceptualization: PC, GLC, and JMCA. Methodology: PC and GLC. Investigation: PC, GLC, and TL. Formal Analysis: PC and GLC. Supervision: VJO and KR. Writing—Original Draft: PC. Writing—Review & Editing: All authors.

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Correspondence to Korneel Rabaey.

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Candry, P., Chadwick, G.L., Caravajal-Arroyo, J.M. et al. Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities. ISME J 17, 2014–2022 (2023). https://doi.org/10.1038/s41396-023-01508-8

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