Scharfe, M. | Search bioRxiv

bioRxiv2022

Transcriptome dynamics of Pseudomonas aeruginosa during transition from replication-uncoupled to -coupled growth

In bacteria, either chromosome duplication is coupled to cell division with only one replication round per cell cycle or DNA is replicated faster than the cells divide thus both processes are uncoupled. Here, we show that the opportunistic pathogen Pseudomonas aeruginosa switches from fast uncoupled to sustained coupled growth when cultivated under standard laboratory conditions. The transition was characterized by fast-paced, sequential changes in transcriptional activity along the ori-ter axis of the chromosome reflecting adaptation to the metabolic needs during both growth phases. Quorum sensing (QS) activity was highest at the onset of the coupled growth phase during which only a quarter of the cells keeps replicating. RNA sequencing of subpopulations of these cultures sorted based on their DNA content, revealed a strong gene dosage effect as well as specific expression patterns for replicating and non-replicating cells. Expression of flagella and mexE, involved in multi drug efflux was restricted to cells that did not replicate, while those that did showed a high activity of the cell division locus and recombination genes. A possible role of QS in the formation of these subpopulations upon switching to coupled growth could be a subject of further research. Significance statementThe coordination of gene expression with the cell cycle has so far been studied only in a handful of bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparing Pseudomonas aeruginosa cultures that differ in their growth mode and number of replicating chromosomes. We further show that cell cycle-specific gene regulation can be principally identified by RNA sequencing of subpopulations from cultures that replicate only once per cell division and that are sorted according to their DNA content. Our approach opens the possibility to study asynchronously growing bacteria from a wide phylogenetic range and thereby enhance our understanding of the evolution of cell-cycle control on the transcriptional level.

microbiology↗

bioRxiv2020

Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom

Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom-derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom-dominated bloom in the German Bight, North Sea. Polysaccharides can be taken up in a selfish mode, where initial hydrolysis is coupled to transport into the periplasm, such that little to no low molecular weight (LMW) products are externally released to the environment. Alternatively, polysaccharides hydrolyzed by cell-surface attached or free extracellular enzymes (external hydrolysis) yield LMW products available to the wider bacterioplankton community. In the early bloom phase, selfish activity was accompanied by low extracellular hydrolysis rates of a few polysaccharides. As the bloom progressed, selfish uptake increased markedly, and external hydrolysis rates increased, but only for a limited range of substrates. The late bloom phase was characterized by high external hydrolysis rates of a broad range of polysaccharides, and reduced selfish uptake of polysaccharides, except for laminarin. Substrate utilization mode is related both to substrate structural complexity and to the bloom-stage dependent composition of the heterotrophic bacterial community. Originality statementThe means by which heterotrophic bacteria cooperate and compete to obtain substrates is a key factor determining the rate and location at which organic matter is cycled in the ocean. Much of this organic matter is high molecular weight (HMW), and must be enzymatically hydrolyzed to smaller pieces to be processed by bacterial communities. Some of these enzyme-producing bacteria are selfish, processing HMW organic matter without releasing low molecular weight (LMW) products to the environment. Other bacteria hydrolyze HMW substrates in a manner that releases LMW products to the wider bacterial community. How these mechanisms of substrate hydrolysis work against a changing background of organic matter supply is unclear. Here, we measured changing rates and mechanisms of substrate processing during the course of a natural phytoplankton bloom in the North Sea. Selfish bacteria generally dominate in the initial bloom stages, but a greater supply of increasingly complex substrates in later bloom stages leads to external hydrolysis of a wider range of substrates, increasing the supply of LMW hydrolysis products to the wider bacterial community.

microbiology↗