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Environ Microbiol. 2016 Jan;18(1):273-87. doi: 10.1111/1462-2920.13019. Epub 2015 Oct 21.

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm.

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Department of Biology, San Diego State University, San Diego, CA, USA.
Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.
Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia.
Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.
Centre for Molecular and Biomedical Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
Division of Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia.


Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.

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