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Background N-acylhomoserine lactones (AHLs) are well-studied signalling molecules produced by some Gram-negative Proteobacteria for bacterial cell-to-cell communication or quorum sensing. We have previously demonstrated the degradation of AHLs by an Antarctic bacterium, Planococcus versutus L10.15T, at low temperature through the production of an AHL lactonase. In this study, we cloned the AHL lactonase gene and characterized the purified novel enzyme. Results Rapid resolution liquid chromatography analysis indicated that purified AidP possesses high AHL-degrading activity on unsubstituted, and 3-oxo substituted homoserine lactones. Liquid chromatography–mass spectrometry analysis confirmed that AidP functions as an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs. Multiple sequence alignment analysis and phylogenetic analysis suggested that the aidP gene encodes a novel AHL lactonase enzyme. The amino acid composition analysis of aidP and the homologous genes suggested that it might be a cold-adapted enzyme, however, the optimum temperature is 28 °C, even though the thermal stability is low (reduced drastically above 32 °C). Branch-site analysis of several aidP genes of Planococcus sp. branch on the phylogenetic trees also showed evidence of episodic positive selection of the gene in cold environments. Furthermore, we demonstrated the effects of covalent and ionic bonding, showing that Zn2+ is important for activity of AidP in vivo. The pectinolytic inhibition assay confirmed that this enzyme attenuated the pathogenicity of the plant pathogen Pectobacterium carotovorum in Chinese cabbage. Conclusion We demonstrated that AidP is effective in attenuating the pathogenicity of P. carotovorum, a plant pathogen that causes soft-rot disease. This anti-quorum sensing agent is an enzyme with low thermal stability that degrades the bacterial signalling molecules (AHLs) that are produced by many pathogens. Since the enzyme is most active below human body temperature (below 28 °C), and lose its activity drastically above 32 °C, the results of a pectinolytic inhibition assay using Chinese cabbage indicated the potential of this anti-quorum sensing agent to be safely applied in the field trials. Electronic supplementary material The online version of this article (10.1186/s12934-018-1024-6) contains supplementary material, which is available to authorized users.

35 páginas, 3 figuras y 2 tablas. -- The definite version is available at http://www.elsevier.com, In this study we analysed three bacterial strains coded L10.10T, A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993T. Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4-30°C, and at pH 4.0-10. The DNA G+C content is 58.2-58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10T, A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10T (LMG 29628T, DSM 101070T)., This work was supported by the University of Malaya (UM) High Impact Research Grants (UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, Grant No. H-50001-A000027; UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/01, Grant No. A-000001-50001)

Quorum sensing (QS) is a regulatory process achieved via cell-to-cell communication that involves release and detection of autoinducers (AIs), and which occurs in a wide range of bacteria. To date, QS has been associated to events of pathogenesis, biofilm formation, and antibiotic resistance in clinical, industrial, and agricultural contexts. The main objective of this study was to characterise the role of N-Acyl homoserine lactone (AHL) type QS in Hafnia alvei FB1, a bacterial strain isolated from frozen vacuum-packed fish paste meatballs, via identification of QS core genes using a genomic approach, followed by comparative transcriptomic profiling between QS-deficient mutants and wild-type strains. H. alvei FB1 is known to produce two types of AHLs, namely, N-(3-oxohexanoyl) homoserine lactone (3OC6-HSL) and N-(3-oxooctanoyl) homoserine lactone (3OC8-HSL). The complete genome sequence of strain FB1 was obtained and a single gene for AHL synthase (halI) and its cognate receptor (halR) were identified. QS-deficient mutants of FB1 were constructed via the λ-Red recombineering method. Removal of the QS genes in strain FB1 affected mainly mechanisms in cell division and nutrient uptake, as well as resistance to a number of antibiotics, which are crucial for survival, adaptation and colonisation of both food and the host gut environment.Impact statementThe Hafnia genus is known as opportunistic pathogen in both nosocomial and community-acquired infections, however, involvement and mechanism of pathogenesis of Hafnia in infection diseases is uncertain. We investigate the role of the signalling molecule, N-acyl homoserine lactones (AHLs), in a Hafnia alvei strain, since AHLs play important roles in pathogenicity, survival or adaptation in other pathogen. This comparative transciptomic study has revealed that AHLs are involved in mechanisms in cell division and nutrient uptake, as well as resistance to a number of antibiotics, which are crucial for survival, adaptation and colonisation of both food and the host gut environment. This finding provides insight and possible strategy to combat this opportunistic pathogen.Data summaryGenome sequence is deposited in NCBI GenBank under accession number CP009706. The transcriptomic data, have been deposited in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds) under accession number GSE93000.

Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of A. alpinus strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s40793-017-0264-0) contains supplementary material, which is available to authorized users.

Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15T, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.

Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron–sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of d-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere. Electronic supplementary material The online version of this article (doi:10.1186/s13568-017-0437-7) contains supplementary material, which is available to authorized users.

DNA methylation, defined by the addition of a methyl group to adenine or cytosine bases in DNA catalyzed by DNA methyltransferases (MTases), is one of the most studied post-replicative DNA modification mechanism in bacteria (Roberts et al., 2003b). The three forms of nucleotide methylation identified to date are: N6-methyladenine(m6A), N4-methylcytosine (m4C), and 5-methylcytosine (m5C) (Gromova and Khoroshaev, 2003). Generally, MTases can be classified into two main groups: as part of a restriction modification (RM) system in which the MTase is associated with a cognate restriction endonuclease (REase) or as a solitary MTase, which as the name suggests, serves the role of an independent MTase (Murphy et al., 2013; Roberts et al., 2015). The RM systems, which are found to occur exclusively in unicellular organisms, can be further classified into four groups based on their subunit composition, recognition sequence specificity, substrate specificity, cofactor requirements, and DNA cleavage positions (Wilson and Murray, 1991; Casadesus and Low, 2006). In brief, Type I RM systems comprise three polypeptides which form a hetero-oligomeric protein complex, namely the R (restriction), M (modification), and S (specificity) subunits, that recognizes asymmetric, and bipartite recognition sequences (Murray, 2000). Type II systems, the most ubiquitous, and simplest systems, are composed of two functionally-independent R and M genes, which are responsible for restriction and methylation activity respectively. The recognition sequences of the Type II systems are most often symmetrical, but can also be asymmetric (Wilson and Murray, 1991). Type III system also consist of two subunits, named res, and mod. The mod subunit can function independently as a MTase, but only methylates one strand of the DNA. The res subunit must form a complex with the mod subunit to express its DNA restriction activity, because the recognition specificity is encoded in the mod subunit (Wilson and Murray, 1991). The recognition sequences of the known Type III systems are asymmetric and four to six bases in length. Furthermore, when known, the res enzyme requires the presence of two unmethylated recognition sites for efficient DNA cleavage (Rao et al., 2013). Lastly, the Type IV systems are restriction enzymes that recognize and cleave only methylated DNA (Vasu and Nagaraja, 2013). The sequence specificities of the Type IV systems are not well studied. MTases can be further sub-classified according to the order of their conserved amino acid motifs, which represent the DNA binding domain, the target recognition domain (TRD) and the catalytic domain (Malone et al., 1995; Jeltsch, 2002). RM systems are often considered as the most primitive defense mechanism of prokaryotes against the invasion of extraneous DNA elements (Wilson and Murray, 1991; Bickle, 2004). However, more recent studies have offered new insights into their additional biological roles, including genomic island stabilization, species identity maintenance, generating, and enhancing genomic diversity for host fitness and adaptability as well as the regulation of gene expression (Vasu and Nagaraja, 2013). The development of Single Molecule Real-Time (SMRT) sequencing technology which enables the simultaneous genome-wide detection of MTase activity during genome sequencing has permitted the rapid detection of novel MTase recognition motifs in various prokaryotes including Helicobacter pylori, Salmonella enterica, Escherichia coli, and Campylobacter coli (Krebes et al., 2014; Forde et al., 2015; Lee et al., 2015; Pirone-Davies et al., 2015; Zautner et al., 2015). These data are important not only for the identification of novel types of MTases, but they also lay the groundwork for the discovery of new biological roles for DNA methylation. Furthermore, these new data on previously characterized methylomes can further extend our understanding of these RM systems. Chania multitudinisentens RB-25T gen. nov., sp. nov. is a fully characterized newly proposed novel genus in the family of Enterobacteriaceae. Isolated in a soil sample collected from a former municipal landfill site, C. multitudinisentens RB-25T was initially misidentified as a member of the Serratia genus (Ee et al., 2014a). Further in-depth investigation later reclassified C. multitudinisentens RB-25T as a novel genus (Ee et al., 2016). To date, C. multitudinisentens RB-25T is only characterized for its quorum sensing properties (the production of C4-HSL, C6-HSL, and 3-oxo-C6-HSL) and its potential chitinolytic activity (Ee et al., 2014a; Lim et al., 2015b). In this study, we report a novel methyltransferase recognition motif in C. multitudinisentens RB-25T, which will serve as the foundation for future investigation of the role of methylation in the genus Chania.

Planococcus kocurii ATCC 43650(T) is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650(T), identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol.

Bacterial quorum sensing signal molecules called N-acylhomoserine lactone (AHL) controls the expression of virulence determinants in many Gram-negative bacteria. We determined AHL production in 22 Aeromonas strains isolated from various infected sites from patients (bile, blood, peritoneal fluid, pus, stool and urine). All isolates produced the two principal AHLs, N-butanoylhomoserine lactone (C4-HSL) and N-hexanoyl homoserine lactone (C6-HSL). Ten isolates also produced additional AHLs. This report is the first documentation of Aeromonas sobria producing C6-HSL and two additional AHLs with N-acyl side chain longer than C(6). Our data provides a better understanding of the mechanism(s) of this environmental bacterium emerging as a human pathogen.

Pseudomonas sp. strain L10.10 (=DSM 101070) is a psychrotolerant bacterium which was isolated from Lagoon Island, Antarctica. Analysis of its complete genome sequence indicates its possible role as a plant-growth promoting bacterium, including nitrogen-fixing ability and indole acetic acid (IAA)-producing trait, with additional suggestion of plant disease prevention attributes via hydrogen cyanide production.