Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics

McDaniel, Elizabeth A.; Moya-Flores, Francisco; Keene Beach, Natalie; Camejo, Pamela Y.; Oyserman, Ben O.; Kizaric, Matthew; Khor, Eng Hoe; Noguera, Daniel R.; McMahon, Katherine D.

doi:10.1128/msystems.00474-21

Title: Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics

Journal Article · Tue Jul 06 00:00:00 EDT 2021 · mSystems

DOI:https://doi.org/10.1128/msystems.00474-21· OSTI ID:1827890

^[1]; Moya-Flores, Francisco ^[2]; Keene Beach, Natalie ^[3]; Camejo, Pamela Y. ^[4]; Oyserman, Ben O. ^[5]; Kizaric, Matthew ^[1]; Khor, Eng Hoe ^[1];

^[6]; McMahon, Katherine D. ^[1]

Univ. of Wisconsin, Madison, WI (United States)
Univ. of Wisconsin, Madison, WI (United States); Geroscience Center for Brain Health and Metabolism (GERO), Santiago (Chile); Millennium Science Initiative, Santiago (Chile)
Univ. of Wisconsin, Madison, WI (United States); Carollo Engineers, Inc., Broomfield, CO (United States)
Univ. of Wisconsin, Madison, WI (United States); Millennium Institute for Integrative Biology (iBio), Santiago (Chile)
Wageningen Univ. (Netherlands); Netherlands Institute of Ecological Research, Wageningen (Netherlands)
Univ. of Wisconsin, Madison, WI (United States); Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. “Candidatus Accumulibacter phosphatis” (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage.

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Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)

Grant/Contract Number:: SC0018409; MCB-1518130

OSTI ID:: 1827890

Journal Information:: mSystems, Vol. 6, Issue 4; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics

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