Comparative Transcriptome Analysis of Shewanella putrefaciens WS13 Biofilms Under Cold Stress

Abstract

Shewanella putrefaciens is a Gram-negative bacterium that can cause seafood spoilage under low-temperature conditions. The bacterium easily forms biofilms to enhance its survival in challenging environments. Our previous research revealed that the biofilm formed by S. putrefaciens WS13 under the low temperature (4 °C) has larger biomass and tighter structure than at an optimum growth temperature (30 °C). In this study, comparative transcriptome analysis was further performed to get insights into the global-level of gene expression in the biofilm formed by S. putrefaciens WS13 under the refrigerating and optimal temperatures using Illumina RNA-Sequencing technique. The results revealed that a total of 761 genes were differentially expressed, of which 497 were significantly up-regulated and 264 were significantly down-regulated (p<0.05). The qRT-PCR results of randomly selected differentially expressed genes (DEGs) confirmed the RNA sequencing results. Comparison of transcriptome data revealed 28 significantly changed metabolic pathways under the cold stress, including the down-regulated chemotaxis, and motility, and up-regulated tryptophan metabolism, histidine biosynthesis, and quorum sensing, which benefited the biofilm formation of S. putrefaciens WS13 under the adverse circumstance. This study provided useful data for better understanding of the biofilm formation of S. putrefaciens, and also laid a theoretical foundation for novel vaccine and drug targets against the severe spoilage bacterium under the cold stress.

The enhanced expression of genes encoding diguanylate cyclases under cold stress contributes to the adhesion and biofilm formation of Shewanella putrefaciens WS13

“…S. putrefaciens has a strong biofilm-forming capability. Our group has found that the formation of biofilm of S. putrefaciens WS13 is conducive to its survival under cold stress ( 6 , 36 ). Further study found that genes such as motA, ppsA , and fabs family expressed in S. putrefaciens WS13 under 4°C help attenuate bacterial motility, enhance bacterial adhesion, and increase biofilm fluidity ( 36 , 37 ), which was beneficial for bacteria to form biofilm under cold stress.…”

“…Our group has found that the formation of biofilm of S. putrefaciens WS13 is conducive to its survival under cold stress ( 6 , 36 ). Further study found that genes such as motA, ppsA , and fabs family expressed in S. putrefaciens WS13 under 4°C help attenuate bacterial motility, enhance bacterial adhesion, and increase biofilm fluidity ( 36 , 37 ), which was beneficial for bacteria to form biofilm under cold stress. Biofilm formation began after bacteria adhered to the surface of the object, and the adhesion of bacteria was regulated by c-di-GMP ( 11 , 25 ).…”

“…Briefly, 1 mL of diluted culture was added into 48-well polystyrene microtiter plates; then, the plates were covered by plastic to avoid evaporative loss. According to bacterial growth curves, after certain cultivation times (6,12,18,24,30,36, and 42 h under 30 • C; 24, 48, 72, 96, 120, 144, 168, 192, 216, 240, and 264 h under 4 • C), biofilms in wells were carefully cleaned three times with 1 mL of 0.01 M sterile phosphate-buffered saline (PBS, pH 7.0) to remove unattached cells. After being dried for 25 min under 60 • C, biofilms were stained with 1 mL of 0.2% (w/v) crystal violet (Sangon Biotech, Co., Ltd., Shanghai, China) for 15 min, then washed and dried as described above.…”

Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita scotiaensis sp. nov.

“…The experiment was performed in triplicate. The 16S RNA gene was used as the reference gene for normalization 52 . The primers used (Supplementary Table 6) in the experiments were designed according to the functional gene sequence using Primer6.0.…”

The Molecular Weaponry Produced by the Bacterium Hafnia alvei in Foods

“…As with other Gram-negative food spoilage bacteria, H. alvei uses an array of N-homoserine lactones as signaling molecules for QS [ 33 , 34 ]. Homoserine lactones (HLs) or N-acyl homoserine lactones (AHLs) are molecules commonly produced by Gram-negative bacteria, including food-borne pathogens such as bacteria of the genus Aeromonas [ 35 ], Shewanella [ 36 ], Clostridium [ 37 ], Pseudomonas [ 38 ], and Salmonella [ 39 ] among others, which constitute a cell density-dependent intercellular signaling mechanism that modulates a great variety of physiological processes, including the production of different virulence factors. Many strains of Enterobacteriaceae isolated from food are able to synthesize AHLs because these molecules are easily detectable from contaminated foods using biosensor strains or biochemical assays.…”