Suchergebnisse

© 2019 The Authors. ; The biological regime of Pseudomonas putida (and any other bacterium) under given environmental conditions results from the hierarchical expression of sets of genes that become turned on and off in response to one or more physicochemical signals. In some cases, such signals are clearly defined, but in many others, cells are exposed to a whole variety of ill‐defined inputs that occur simultaneously. Transcriptomic analyses of bacteria passed from a reference condition to a complex niche can thus expose both the type of signals that they experience during the transition and the functions involved in adaptation to the new scenario. In this article, we describe a complete protocol for generation of transcriptomes aimed at monitoring the physiological shift of P. putida between two divergent settings using as a simple case study the change between homogeneous, planktonic lifestyle in a liquid medium and growth on the surface of an agar plate. To this end, RNA was collected from P. putidaKT2440 cells at various times after growth in either condition, and the genome‐wide transcriptional outputs were analysed. While the role of individual genes needs to be verified on a case‐by‐case basis, a gross inspection of the resulting profiles suggested cells that are cultured on solid media consistently had a higher translational and metabolic activity, stopped production of flagella and were conspicuously exposed to a strong oxidative stress. The herein described methodology is generally applicable to other circumstances for diagnosing lifestyle determinants of interest. ; This work was funded by the HELIOS Project of the Spanish Ministry of Science BIO 2015-66960-C3-2-R (MINECO/FEDER), the ARISYS (ERC-2012-ADG-322797), EmPowerPutida (EU-H2020- BIOTEC-2014-2015-633 5536) and MADONNA (H2020-FET-OPENRIA-2017-1-766975) contracts of the European Union, the InGEMICS-CM (B2017/BMD-3691) contract of the Comunidad de Madrid (FSE, FECER) and NIH grant R01GM123609

AbstractParticulate organic carbon settling through the marine water column is a key process that regulates the global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents—setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally using millifluidic devices that, although bacterial motility is essential for effective colonization of a particle leaking organic nutrients into the water column, chemotaxis specifically benefits at intermediate and higher settling velocities to navigate the particle boundary layer during the brief window of opportunity provided by a passing particle. We develop an individual-based model that simulates the encounter and attachment of bacterial cells with leaking marine particles to systematically evaluate the role of different parameters associated with bacterial run-and-tumble motility. We further use this model to explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We find that the porous microstructure facilitates additional colonization by chemotactic and motile bacteria, and fundamentally alters the way nonmotile cells interact with particles due to streamlines intersecting with the particle surface.

We thank the patients and staff at each of the contributing centres for their involvement, time and patience in sample collection. This study was supported by grants from the UK Natural Environment Research Council (NE/H019456/1) and the Wellcome Trust (WT 098051). AWW receives core funding support from the Scottish Government's Rural and Environment Science and Analytical Services (RESAS) division. AA and GO received support from the Dartmouth Translational Research Core (CFF RDP STANTO15R0) for acquiring samples. ; Peer reviewed ; Publisher PDF