Transcriptome Analysis of Early Surface-Associated Growth of Shewanella oneidensis MR-1

Abstract

Bacterial biofilm formation starts with single cells attaching to a surface, however, little is known about the initial attachment steps and the adaptation to the surface-associated life style. Here, we describe a hydrodynamic system that allows easy harvest of cells at very early biofilm stages. Using the metal ion-reducing gammaproteobacterium Shewanella oneidensis MR-1 as a model organism, we analyzed the transcriptional changes occurring during surface-associated growth between 15 and 60 minutes after attachment. 230 genes were significantly upregulated and 333 were downregulated by a factor of ≥2. Main functional categories of the corresponding gene products comprise metabolism, uptake and transport, regulation, and hypothetical proteins. Among the genes highly upregulated those implicated in iron uptake are highly overrepresented, strongly indicating that S. oneidensis MR-1 has a high demand for iron during surface attachment and initial biofilm stages. Subsequent microscopic analysis of biofilm formation under hydrodynamic conditions revealed that addition of Fe(II) significantly stimulated biofilm formation of S. oneidensis MR-1 while planktonic growth was not affected. Our approach to harvest cells for transcriptional analysis of early biofilm stages is expected to be easily adapted to other bacterial species.

Iron Triggers λSo Prophage Induction and Release of Extracellular DNA in Shewanella oneidensis MR-1 Biofilms

“…In a previous study, we demonstrated that early surface-associated growth induces the expression of genes belonging to the putative OxyR (oxidative stress defense regulator) and Fur (ferric uptake regulator) regulons in S. oneidensis MR-1 (48). Based on these and ⌬recA deletion mutants (recA Ϫ) after UV exposure (ϩ) or without UV exposure (Ϫ).…”

“…If required, FeCl 2 or desferrioxamine mesylate salt was added to the medium reservoir. For protein sampling, biofilm cells were cultivated in 50-ml syringes on glass beads under constant medium flow and harvested as described earlier (48).…”

Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation

“…It is likely that the physiological response is an energetically costly process, requiring complex regulatory changes. For example, the response leading to S. oneidensis biofilm formation depends on the coordinated expression of multiple multisubunit structures, such as pili and adhesins, as well as large shifts in metabolism (46). Similar complex levels of regulation are probably necessary to control the extension of the outer membrane in the form of nanowires.…”

Influence of hydrodynamics on the growth kinetics of glass-adhering Pseudomonas putida cells through a parallel plate flow chamber

“…Recently, G€ odeke et al 11 investigated the bacterial surface-associated growth in a flow chamber. They revealed several transcriptional changes during the earlier stage of cells surface colonization, and especially the expression changes in functional genes coding for transport and conversion of carbohydrates, amino-acid transport and metabolism, lipid metabolism, gluconate catabolism, and also phage genes regulation.…”

“…To the best of our knowledge, few studies have been indeed performed to investigate specifically the early stage of growth of initially adhering bacteria or cells on solid surfaces [9][10][11] in terms of growth kinetics and its coupling with the local hydrodynamics.…”