The transcriptional programme of Salmonella enterica serovar Typhimurium reveals a key role for tryptophan metabolism in biofilms

<p>Abstract</p> <p>Background</p> <p>Biofilm formation enhances the capacity of pathogenic <it>Salmonella </it>bacteria to survive stresses that are commonly encountered within food processing and during host infection. The persistence of <it>Salmonella </it>within the food chain has become a major health concern, as biofilms can serve as a reservoir for the contamination of food products. While the molecular mechanisms required for the survival of bacteria on surfaces are not fully understood, transcriptional studies of other bacteria have demonstrated that biofilm growth triggers the expression of specific sets of genes, compared with planktonic cells. Until now, most gene expression studies of <it>Salmonella </it>have focused on the effect of infection-relevant stressors on virulence or the comparison of mutant and wild-type bacteria. However little is known about the physiological responses taking place inside a <it>Salmonella </it>biofilm.</p> <p>Results</p> <p>We have determined the transcriptomic and proteomic profiles of biofilms of <it>Salmonella enterica </it>serovar Typhimurium. We discovered that 124 detectable proteins were differentially expressed in the biofilm compared with planktonic cells, and that 10% of the <it>S</it>. Typhimurium genome (433 genes) showed a 2-fold or more change in the biofilm compared with planktonic cells. The genes that were significantly up-regulated implicated certain cellular processes in biofilm development including amino acid metabolism, cell motility, global regulation and tolerance to stress. We found that the most highly down-regulated genes in the biofilm were located on <it>Salmonella </it>Pathogenicity Island 2 (SPI2), and that a functional SPI2 secretion system regulator (<it>ssrA</it>) was required for <it>S</it>. Typhimurium biofilm formation. We identified STM0341 as a gene of unknown function that was needed for biofilm growth. Genes involved in tryptophan (<it>trp</it>) biosynthesis and transport were up-regulated in the biofilm. Deletion of <it>trpE </it>led to decreased bacterial attachment and this biofilm defect was restored by exogenous tryptophan or indole.</p> <p>Conclusions</p> <p>Biofilm growth of <it>S</it>. Typhimurium causes distinct changes in gene and protein expression. Our results show that aromatic amino acids make an important contribution to biofilm formation and reveal a link between SPI2 expression and surface-associated growth in <it>S</it>. Typhimurium.</p

Biodiversity of Reef-Building, Scleractinian Corals

Zooxanthellate scleractinian corals are moderately well-known for shallow reef habitats, but not for mesophotic depths (>30 m) that are relatively difficult to access. Mesophotic habitats are light-limited, with different hydrodynamics and sedimentation processes, which result in growth forms that are often difficult to classify using traditional schemes based largely on shallow reef specimens. We analyzed published data and museum records, using specimen-based records to minimize classification issues, finding 53 mesophotic species in the western Atlantic Ocean (85% of total species) and 338 in the Indo-Pacific (45%). Only four species were recorded exclusively below 30 m depth, while the great majority were common shallow reef taxa. Over 96% of western Atlantic and 82% of Indo-Pacific genera and most coral lineages were represented below 30 m depth. In the Indo-Pacific, species and genus richness varied widely between regions and were significantly correlated with shallow reef species richness. Overall, species richness decreased steadily with increasing depth, with little evidence for distinct faunal boundaries: 157 species occurred >= 60 m and 31 deeper than 100 m, with species occurrence only moderately related to phylogeny. Our knowledge of mesophotic biodiversity is rapidly changing as more regions are documented and new molecular techniques suggest taxonomic revisions and resolve deepwater cryptic species. We conclude that mesophotic scleractinian fauna are largely a subset of shallow scleractinian fauna, comprising a significant proportion of coral species and most genera, with the potential to play a significant role in lineage preservation and the future of coral reefs