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

Barr, Jeremy J. and Dutilh, Bas E. and Skennerton, Connor T. and Fukushima, Toshikazu and Hastie, Marcus L. and Gorman, Jeffrey J. and Tyson, Gene W. and Bond, Philip L. (2016) Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm. Environmental Microbiology, 18 (1). pp. 273-287. ISSN 1462-2912. https://resolver.caltech.edu/CaltechAUTHORS:20150824-142733864

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Abstract

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 (EBPR). 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 2,022 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 (EPS) 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1111/1462-2920.13019DOIArticle
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13019/abstractPublisherArticle
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13019/suppinfoPublisherSupporting Information
ORCID:
AuthorORCID
Skennerton, Connor T.0000-0003-1320-4873
Tyson, Gene W.0000-0001-8559-9427
Additional Information:© 2015 John Wiley & Sons, Inc. This work was funded by the Environmental Biotechnology Cooperative Research Centre (EBCRC), which was established and funded by the Australian Government, together with industry and university partners. JJB acknowledges EBCRC for funding of a Ph.D. scholarship. PLB acknowledges EBCRC, Waste Technologies of Australia, The University of Queensland, and the Queensland Government Smart State Fellowship Program for funding of a senior research fellowship. Access to proteomic infrastructure in the QIMR Berghofer Protein Discovery Centre was made possible by funding from Bioplatforms Australia and the Queensland State Government provided through the Australian Government National Collaborative Infrastructure Scheme (NCRIS) and Education Investment Fund (EIF). The authors thank Jolein Gloerich and Hans Wessels of the Radboud Proteomics Centre for their help in analyzing the proteomics data. The authors declare no conflict of interest.
Funders:
Funding AgencyGrant Number
Australian GovernmentUNSPECIFIED
Environmental Biotechnology Cooperative Research Centre (EBCRC)UNSPECIFIED
Waste Technologies of AustraliaUNSPECIFIED
University of QueenslandUNSPECIFIED
Queensland Government Smart State Fellowship ProgramUNSPECIFIED
Bioplatforms AustraliaUNSPECIFIED
Issue or Number:1
Record Number:CaltechAUTHORS:20150824-142733864
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20150824-142733864
Official Citation:Barr, J. J., Dutilh, B. E., Skennerton, C. T., Fukushima, T., Hastie, M. L., Gorman, J. J., Tyson, G. W. and Bond, P. L. (2016), Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environ Microbiol, 18: 273–287. doi:10.1111/1462-2920.13019
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:59859
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 Aug 2015 22:44
Last Modified:09 Mar 2020 13:19

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