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RNA-seq of Escherichia coli MG1655 and SR under fluctuating ammonia availability (limitation-depletion)

ABSTRACT: In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs which result in production yield losses. This study is focused on transcriptional changes due to fluctuating ammonia supply, while sampling a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). A previously created mutant E.coli SR was used to limit the reaction to environmntal influences via knock-out of stringent response. E. coli WT revealed highly diverging short-term transcriptional responses in ammonia fluctuation compared E. coli SR.

ORGANISM(S): Escherichia coli

PROVIDER: GSE158198 | GEO | 2021/05/05

REPOSITORIES: GEO

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Project description:Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO2- entering the reactor from an upstream trickling filter (Wells et al 2009). Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO2- production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct ‘Nitrosomonas-like’ lineage dominated in activated sludge. Prior time series indicated that this ‘Nitrosomonas-like’ lineage was dominant when NO2- levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO2- levels were high. This is consistent with the hypothesis that NO2- production may co-occur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor. Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors.

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RNA-seq of Escherichia coli MG1655 and SR under fluctuating ammonia availability (limitation-depletion)

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