Main menu

Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics


Microbial communities in their natural habitats consist of closely related populations 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’ 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 co-exist in full-scale wastewater treatment plants and lab-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 composition.

Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of co-existing Accumulibacter clades 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 reads. We identified core and accessory genes to investigate how gene expression patterns differ among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may differ between Accumulibacter clades and provide key functional insights into this biotechnologically significant microbial lineage.

IMPORTANCECandidatus Accumulibacter phosphatis’ is a model polyphosphate accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process.

Within the Accumulibacter lineage, several similar but diverging clades are defined by the polyphosphate kinase (ppk1) locus sequence identity. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen cycling capabilities. However, such hypotheses have largely been made based on gene-content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems.

Here, we performed time-series genome-resolved metatranscriptomics to explore gene expression patterns of co-existing Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.

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

入门指南

购买 MinION 启动包 Nanopore 商城 测序服务提供商 全球代理商

纳米孔技术

订阅 Nanopore 更新 资源库及发表刊物 什么是 Nanopore 社区

关于 Oxford Nanopore

新闻 公司历程 可持续发展 领导团队 媒体资源和联系方式 投资者 合作者 在 Oxford Nanopore 工作 职位空缺 商业信息 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Chinese flag