Identification of two different chemosensory pathways in representatives of the genus Halomonas

Abstract

BackgroundSpecies of the genus Halomonas are salt-tolerant organisms that have a versatile metabolism and can degrade a variety of xenobiotic compounds, utilizing them as their sole carbon source. In this study, we examined the genome of a Halomonas isolate from a hydrocarbon-contaminated site to search for chemosensory genes that might be responsible for the observed chemotactic behavior of this organism as well as for other responses to environmental cues.ResultsUsing genome-wide comparative tools, our isolate was identified as a strain of Halomonas titanicae (strain KHS3), together with two other Halomonas strains with available genomes that had not been previously identified at a species level.The search for the main components of chemosensory pathways resulted in the identification of two clusters of chemosensory genes and a total of twenty-five chemoreceptor genes.One of the gene clusters is very similar to the che cluster from Escherichia coli and, presumably, it is responsible for the chemotactic behavior towards a variety of compounds. This gene cluster is present in 47 out of 56 analyzed Halomonas strains with available genomes.A second che-like cluster includes a gene coding for a diguanylate cyclase with a phosphotransfer and two receiver domains, as well as a gene coding for a chemoreceptor with a longer cytoplasmic domain than the other twenty-four. This seemingly independent pathway resembles the wsp pathway from Pseudomonas aeruginosa although it also presents several differences in gene order and domain composition. This second chemosensory gene cluster is only present in a sub-group within the genus Halomonas. Moreover, remarkably similar gene clusters are also found in some orders of Proteobacteria phylogenetically more distant from the Oceanospirillales, suggesting the occurrence of lateral transfer events.ConclusionsChemosensory pathways were investigated within the genus Halomonas. A canonical chemotaxis pathway, controlled by a variable number of chemoreceptors, is widespread among Halomonas species. A second chemosensory pathway of unique organization that involves some type of c-di-GMP signaling was found to be present only in one branch of the genus, as well as in other proteobacterial lineages.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4655-4) contains supplementary material, which is available to authorized users.

Effects of Halophyte Root Exudates and Their Components on Chemotaxis, Biofilm Formation and Colonization of the Halophilic Bacterium Halomonas Anticariensis FP35T

“…This gene cluster seems to govern the chemotactic behavior of FP35 T and it is very similar to the cluster from Escherichia coli including the cheA gene. Similar results were previously described for this strain and other species from the genus Halomonas [27]. Given its importance in the chemotaxis pathway of other bacteria, the cheA gene, through its disruption in strain FP35 T , was found to play a crucial role in chemotactic responses to environmental hydrocarbon pollutants [25].…”

“…Though extensively studied in model organisms such as Escherichia coli and Pseudomonas spp. [19], little is known about these chemotactic bacterial systems in halophilic bacteria such as those of the genus Halomonas [25][26][27], which have, however, been studied in relation to Salicornia root colonization [63]. We assayed the motility of bacteria belonging to the genus Halomonas that were isolated from the halophyte rhizosphere.…”

“…These findings point to the significance of salt concentrations in the chemotaxis system and of the chemotaxis responses of H. anticariensis FP35 T to different substances found in the soil. To the best of our knowledge, only few studies analyse the chemotactic behaviour of Halomonas strains using swimming assays with times of incubation higher than 24 h [27,66].…”

“…Ling et al [23] have reported that organic acids in watermelon root exudates recruit Paenibacillus polymyxa SQR-21, while Rudrappa et al have described how malic acid in plant roots chemically attracts Bacillus subtilis FB17 [24]. However, little is known about the responses of halophilic bacteria to chemical and natural compounds or their chemotaxis machinery, with only a few recent studies describing the chemotaxis-mediated responses of H. anticariensis FP35 T to environmental pollutants [25] and analysing the genome of Halomonas strains to search for chemosensory genes and the chemosensory pathways within the genus Halomonas [26,27].…”

Identification and characterization of ectoine-producing bacteria isolated from Can Gio mangrove soil in Vietnam

“…Furthermore, Halomonas spp. are moderate halophiles, requiring salt concentrations between 3 and 15% (w/v) for growth (Mata et al 2002;Gasperotti et al 2018). Several Halomonas strains have been considered as ideal candidates for potential biotechnological applications, including degradation of organic pollutants and production of compatible solutes, biopolymer, and enzymes (Margesin and Schinner 2001).…”