Biology subjects

Oyserman, B. O.

Publications and source records attributed to Oyserman, B. O..

3 recordsLinked to original sources

bioRxiv2018

Integrated ‘omic’ analyses provide evidence that a Ca. Accumulibacter phosphatis strain performs denitrification under micro-aerobic conditions

The unique and complex metabolism of Candidatus Accumulibacter phosphatis has been used for decades for efficiently removing phosphorus during wastewater treatment in reactor configurations that expose the activated sludge to cycles of anaerobic and aerobic conditions. The ability of Accumulibacter to grow and remove phosphorus during cyclic anaerobic and anoxic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, elucidating the role of Accumulibacter in this process has been challenging, since experimental research describes contradictory findings and none of the published Accumulibacter genomes show the existence of a complete pathway for denitrification. In this study, we use an integrated omics analysis to elucidate the physiology of an Accumulibacter strain enriched in a reactor operated under cyclic anaerobic and micro-aerobic conditions. The reactors performance suggested the ability of the enriched Accumulibacter (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under micro-aerobic conditions. A draft genome of this organism was assembled from metagenomic reads (hereafter referred to as Accumulibacter UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full denitrification pathway. The observed patterns of transcript abundance showed evidence of co-regulation of the denitrifying genes along with a cbb3 cytochrome, which is characterized as having high affinity for oxygen, thus supporting the hypothesis that UW-LDO-IC can simultaneously respire nitrate and oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcriptional level regulation of the expression of both denitrifying and respiratory pathways in Accumulibacter UW-LDO-IC. Taken together, the omics analysis provides strong evidence that Accumulibacter UW-LDO-IC simultaneously uses oxygen and nitrate as electron acceptors under micro-aerobic conditions.\n\nIMPORTANCECandidatus Accumulibater phosphatis is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, micro-aerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our study provides strong genomics-based evidence that Accumulibacter is not only the main organism contributing to phosphorus removal under micro-aerobic conditions, but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.

microbiology↗

bioRxiv2018

acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively-synthesized Retinal

Freshwater lakes harbor complex microbial communities, but these ecosystems are often dominated by acI Actinobacteria from three clades (acI-A, acI-B, acI-C). Members of this cosmopolitan lineage are proposed to bolster heterotrophic growth using phototrophy because their genomes encode actino-opsins (actR). This model has been difficult to experimentally validate because acI are not consistently culturable. In this study, using genomes from single cells and metagenomes, we provide a detailed biosynthetic route for many acI-A and -B members to synthesize retinal and its carotenoid precursors. Accordingly, these acI should be able to natively assemble light-driven actinorhodopsins (holo-ActR) to pump protons, in contrast to acI-C members and other bacteria that encode opsins but lack retinal-production machinery. Moreover, we show that all acI clades contain genes for a complex carotenoid pathway that starts with retinal precursors. Transcription analysis of acI in a eutrophic lake shows that all retinal and carotenoid pathway operons are transcribed and that actR is among the most highly-transcribed of all acI genes. Furthermore, heterologous expression of retinal pathway genes shows that lycopene, retinal, and ActR can be made. Model cells producing ActR and the key acI retinal-producing {beta}-carotene oxygenase formed acI-holo-ActR and acidified solution during illumination. Our results prove that acI containing both ActR and retinal-production enzymes have the capacity to natively synthesize a green light-dependent outward proton-pumping rhodopsin.\n\nIMPORTANCEMicrobes play critical roles in determining the quality of freshwater ecosystems that are vital to human civilization. Because acI Actinobacteria are ubiquitous and abundant in freshwater lakes, clarifying their ecophysiology is a major step in determining the contributions that they make to nitrogen and carbon cycling. Without accurate knowledge of these cycles, freshwater systems cannot be incorporated into climate change models, ecosystem imbalances cannot be predicted, and policy for service disruption cannot be planned. Our work fills major gaps in microbial light utilization, secondary metabolite production, and energy cycling in freshwater habitats.

microbiology↗

bioRxiv2017

High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage

An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the \"seed set framework\", which computes the set of compounds that an organism must acquire from its environment (1), enables computational analysis of metabolic reconstructions, while providing new insights into a microbes metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater Actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support to the hypothesis that members of the acI are photoheterotrophs.\n\nImportanceThe metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organisms metabolic pathways, or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more intensive metabolic reconstruction efforts, and also provide new hypotheses about the specific contributions microbes make to ecosystem-scale metabolic processes.

microbiology↗