Comparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in Janthinobacterium.

Violacein has different bioactive properties conferring distinct selective advantages, such as defense from predation and interspecific competition. Adaptation of Janthinobacterium to diverse habitats likely leads to variation in violacein production among phylogenetically closely related species inhabiting different environments, yet genomic mechanisms and the influence of adaptive evolution underpinning violacein biosynthesis in Janthinobacterium are not clear. In this study, we performed genome sequencing, comparative genomic analysis, and phenotypic characterization to investigate genomic factors regulating violacein production in nine Janthinobacterium strains, including a type strain from soil and eight strains we isolated from terrestrial subsurface sediment and groundwater. Results show that although all nine Janthinobacterium strains are phylogenetically closely related and contain genes essential for violacein biosynthesis, they vary in carbon usage and violacein production. Sediment and groundwater strains are weak violacein producers and possess far fewer secondary metabolite biosynthesis genes, indicating genome adaptation compared to soil strains. Further examination suggests that quorum sensing (QS) may play an important role in regulating violacein in Janthinobacterium: the strains exhibiting strong potential in violacein production possess both N-acyl-homoserine lactone (AHL) QS and Janthinobacterium QS (JQS) systems in their genomes, while weaker violacein-producing strains harbor only the JQS system. Preliminary tests of spent media of two Janthinobacterium strains possessing both AHL QS and JQS systems support the potential role of AHLs in inducing violacein production in Janthinobacterium. Overall, results from this study reveal potential genomic mechanisms involved in violacein biosynthesis in Janthinobacterium and provide insights into evolution of Janthinobacterium for adaptation to oligotrophic terrestrial subsurface environment. IMPORTANCE Phylogenetically closely related bacteria can thrive in diverse environmental habitats due to adaptive evolution. Genomic changes resulting from adaptive evolution lead to variations in cellular function, metabolism, and secondary metabolite biosynthesis. The most well-known secondary metabolite produced by Janthinobacterium is the purple-violet pigment violacein. To date, the mechanisms of induction of violacein biosynthesis in Janthinobacterium is not clear. Comparative genome analysis of closely related Janthinobacterium strains isolated from different environmental habitats not only reveals potential mechanisms involved in induction of violacein production by Janthinobacterium but also provides insights into the survival strategy of Janthinobacterium for adaptation to oligotrophic terrestrial subsurface environment.

Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism.

BACKGROUND: Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment. METHODS: Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria. RESULTS: 16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch. CONCLUSIONS: The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions.

Biosynthesis, Characterization and Antibacterial Application of Novel Silver Nanoparticles against Drug Resistant Pathogenic Klebsiella pneumoniae and Salmonella Enteritidis.

The present study highlights the biosynthesis of silver nanoparticles (AgNPs) using culture supernatant of Massilia sp. MAHUQ-52 as well as the antimicrobial application of synthesized AgNPs against multi-drug resistant pathogenic Klebsiella pneumoniae and Salmonella Enteritidis. Well-defined AgNPs formation occurred from the reaction mixture of cell-free supernatant and silver nitrate (AgNO3) solution within 48 h of incubation. UV-visible spectroscopy analysis showed a strong peak at 435 nm, which corresponds to the surface plasmon resonance of AgNPs. The synthesized AgNPs were characterized by FE-TEM, EDX, XRD, DLS and FT-IR. From FE-TEM analysis, it was found that most of the particles were spherical shape, and the size of synthesized nanoparticles (NPs) was 15-55 nm. EDX spectrum revealed a strong silver signal at 3 keV. XRD analysis determined the crystalline, pure, face-centered cubic AgNPs. FT-IR analysis identified various functional molecules that may be involved with the synthesis and stabilization of AgNPs. The antimicrobial activity of Massilia sp. MAHUQ-52 mediated synthesized AgNPs was determined using the disk diffusion method against K. pneumoniae and S. Enteritidis. Biosynthesized AgNPs showed strong antimicrobial activity against both K. pneumoniae and S. Enteritidis. The MICs of synthesized AgNPs against K. pneumoniae and S. Enteritidis were 12.5 and 25.0 µg/mL, respectively. The MBC of biosynthesized AgNPs against both pathogens was 50.0 µg/mL. From FE-SEM analysis, it was found that the AgNPs-treated cells showed morphological changes with irregular and damaged cell walls that culminated in cell death.

Degradation of epigallocatechin and epicatechin gallates by a novel tannase TanHcw from Herbaspirillum camelliae.

BACKGROUND: Herbaspirillum camelliae is a gram-negative endophyte isolated from the tea plant. Both strains WT00C and WT00F were found to hydrolyze epigallocatechin-3-gallate (EGCG) and epicatechin-3-gallate (ECG) to release gallic acid (GA) and display tannase activity. However, no tannase gene was annotated in the genome of H. camelliae WT00C. RESULTS: The 39 kDa protein, annotated as the prolyl oligopeptidase in the NCBI database, was finally identified as a novel tannase. Its gene was cloned, and the enzyme was expressed in E. coli and purified to homogeneity. Moreover, enzymatic characterizations of this novel tannase named TanHcw were studied. TanHcw was a secretary enzyme with a Sec/SPI signal peptide of 48 amino acids at the N-terminus, and it catalyzed the degradation of tannin, methyl gallate (MG), epigallocatechin-3-gallate (EGCG) and epicatechin-3-gallate (ECG). The optimal temperature and pH of TanHcw activities were 30 °C, pH 6.0 for MG and 40 °C, pH 7.0 for both EGCG and ECG. Na+, K+ Mn2+ and Triton-X100, Tween80 increased the enzyme activity of TanHcw, whereas Zn2+, Mg2+, Hg2+, EMSO, EDTA and ß-mercaptoethanol inhibited enzyme activity. Km, kcat and kcat /Km of TanHcw were 0.30 mM, 37.84 s-1, 130.67 mM-1 s-1 for EGCG, 0.33 mM, 34.59 s-1, 105.01 mM-1 s-1 for ECG and 0.82 mM, 14.64 s-1, 18.17 mM-1 s-1 for MG, respectively. CONCLUSION: A novel tannase TanHcw from H. camelliae has been identified and characterized. The biological properties of TanHcw suggest that it plays a crucial role in the specific colonization of H. camelliae in tea plants. Discovery of the tannase TanHcw in this study gives us a reasonable explanation for the host specificity of H. camelliae. In addition, studying the characteristics of this enzyme offers the possibility of further defining its potential in industrial application.

Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae.

We isolated two new soil bacteria: ONC3T (from garden soil in NC, USA; LMG 31738T=NRRL B-65553T) and M1T (from farmed soil in MI, USA; NRRL B-65551T=ATCC TSD-197T=LMG 31739T) and characterized their metabolic phenotype based on Biolog, MALDI-TOF MS and fatty acid analyses, and compared 16S rRNA and whole genome sequences to other members of the Oxalobacteraceae after sequencing on an Illumina Nextera platform. Based on the results of 16S rRNA sequence analysis, ONC3T shows the highest sequence similarity to Massilia solisilvae J18T (97.8 %), Massilia terrae J11T (97.7 %) and Massilia agilis J9T (97.3 %). Strain M1T is most closely related to Noviherbaspirillum denitrificans TSA40T, Noviherbaspirillum agri K-1-15T and Noviherbaspirillum autotrophicum TSA66T (sequence identity of 98.2, 98.0 and 97.8 %, respectively). The whole genome of ONC3T has an assembled size of 5.62 Mbp, a G+C content of 63.8 mol% and contains 5104 protein-coding sequences, 56 tRNA genes and two rRNA operons. The genome of M1T has a length of 4.71 MBp, a G+C content of 63.81 mol% and includes 4967 protein-coding genes, two rRNA operons and 44 tRNA genes. Whole genome comparisons identified Massilia sp. WG5 with a 79.3 % average nucleotide identity (ANI) and 22.6 % digital DNA-DNA hybridization (dDDH), and Massilia sp. UBA11196 with 78.2 % average amino acid identity (AAI) as the most closely related species to ONC3T. M1T is most closely related to N. autotrophicum TSA66T with an ANI of 80.27 %, or N. denitrificans TSA40T with a dDDH of 22.3 %. The application of community-accepted standards such as <98.7 % in 16S sequence similarity and <95-96 % ANI or 70 % DDH support the classification of Massilia horti ONC3T and Noviherbaspirillum arenae M1T as novel species within the Oxalobacteraceae.

Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway.

Empedopeptins-eight amino acid cyclic lipopeptides-are calcium-dependent antibiotics that act against Gram-positive bacteria such as Staphylococcus aureus by inhibiting cell wall biosynthesis. However, to date, the biosynthetic mechanism of the empedopeptins has not been well identified. Through comparative genomics and metabolomics analysis, we identified empedopeptin and its new analogs from a marine bacterium, Massilia sp. YMA4. We then unveiled the empedopeptin biosynthetic gene cluster. The core nonribosomal peptide gene null-mutant strains (ΔempC, ΔempD, and ΔempE) could not produce empedopeptin, while dioxygenase gene null-mutant strains (ΔempA and ΔempB) produced several unique empedopeptin analogs. However, the antibiotic activity of ΔempA and ΔempB was significantly reduced compared with the wild-type, demonstrating that the hydroxylated amino acid residues of empedopeptin and its analogs are important to their antibiotic activity. Furthermore, we found seven bacterial strains that could produce empedopeptin-like cyclic lipopeptides using a genome mining approach. In summary, this study demonstrated that an integrated omics strategy can facilitate the discovery of potential bioactive metabolites from microbial sources without further isolation and purification.

Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.

A Gram-reaction-negative, strictly aerobic, betaproteobacterial strain, designated SAP-35T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea, and its taxonomic status was examined by a polyphasic approach. Cells of the organism were non-sporulating, motile rods and grew at 4-30 °C, pH 6-7 and in the absence of NaCl. 16S rRNA gene- and whole genome-based phylogenetic analyses showed that strain SAP-35T belonged to the family Oxalobacteraceae and was closely related to Rugamonas rivuli (98.9% 16S rRNA gene sequence similarity) and Rugamonas aquatica (98.4%). The phylogenomic clustering and average amino acid identity values supported that strain SAP-35T belonged to the genus Duganella and two Rugamonas species should be transferred to the genus Duganella. The major isoprenoid quinone of the isolate was Q-8. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were summed feature 3, C16:0 and C17:0 cyclo. The G + C content of genome was 64.9%. The average nucleotide identity and dDDH values between strain SAP-35T and the members of the genera Rugamonas and Duganella were < 85.1% and < 49%, respectively. Based on the combined data presented here, strain SAP-35T (= KCTC 72227T = NBRC 113903T) represents a novel species of the genus Duganella, for which the name Duganella aceris sp. nov. is proposed. Also, Rugamonas aquatica Lu et al. (Int J Syst Evol Microbiol 70: 3328-3334, 2020) and Rugamonas aquatica Lu et al. 2020 are reclassified as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.

Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil.

An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. pinisoli T33T (98.8% sequence similarity), M. putida 6NM-7T (98.6%), M. arvi THG-RS2OT (98.5%), M. phosphatilytica 12-OD1T (98.3%) and M. niastensis 5516S-1T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis-9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain TW-1T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1T possessed inhibitory activity against Gram-negative pathogens (Escherichia coli and Pseudomonas aeruginosa). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1T represents novel species in the genus Massilia, for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1T (= KACC 21627T = NBRC 114363T).

First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and Their Comparative Genome Analysis.

We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in Göttingen. The strains were phylogenetically classified by average nucleotide identity (ANI) analysis and showed a species assignment to J. lividum with 97.72% (EIF1) and 97.66% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species J. lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a nonribosomal peptide synthetase cluster with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites.

Identification and characterization of a novel extracellular polyhydroxyalkanoate depolymerase in the complete genome sequence of Undibacterium sp. KW1 and YM2 strains.

Polyhydroxyalkanoate (PHA) is a biodegradable polymer that is synthesized by a wide range of microorganisms. One of the derivatives of PHA, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) has flexible material properties and low melting temperature. We have previously demonstrated that PHBH is degradable in a freshwater environment via the formation of biofilm on the surface of the PHBH film. Undibacterium sp. KW1 and YM2, which were isolated from the biofilm present on the PHBH film in the freshwater sample, were shown to have PHBH-degrading activity. In this study, the complete genome sequence of KW1 and YM2 revealed that the extracellular PHA depolymerase gene, designated as phaZUD, was present in their chromosomes. Sequence analysis revealed that PhaZUD contained four domains: a signal peptide, catalytic domain, linker domain, and substrate-binding domain. Escherichia coli harboring a PhaZUD-expressing plasmid showed PHBH-degrading activity in LB medium containing 1 wt% PHBH powder. The recombinant His-tagged PhaZUD from KW1 and YM2 was purified from the culture supernatant and shown to have PHBH-degrading activity at the optimum temperature of 35 and 40°C, respectively. When the degradation product in the PHBH solution was treated with PhaZUD and assayed by LC-TOF-MS, we detected various oligomer structures, but no more than pentamers, which consist of 3-hydroxybutyrate and 3-hydroxyhexanoate. These results demonstrated that PhaZUD may have an endo-type extracellular PHA depolymerase activity.

Interruption of Aspergillus niger spore germination by the bacterially produced secondary metabolite collimomycin.

Collimonas fungivorans Ter331 (CfTer331) is a soil bacterium that produces collimomycin, a secondary metabolite that inhibits the vegetative growth of fungi. Here we show that CfTer331 can also interfere with fungal spore germination and that collimomycin biosynthesis is required for this activity. More specifically, in co-cultures of Aspergillus niger N402 (AnN402) co-nidiospores with CfTer331, the rate of transition from the isotropic to polarized stage of the germination process was reduced and the relatively few AnN402 conidiospores that completed the germination process were less likely to survive than those that were arrested in the isotropic phase. By contrast, a collimomycin-deficient mutant of CfTer331 had no effect on germination: in its presence, as in the absence or delayed presence of CfTer331, unhindered germination of conidiospores allowed rapid establishment of AnN402 mycelium and the subsequent acidification of the culture medium to the detriment of any bacteria present. However, when challenged early enough with CfTer331, the collimomycin-dependent arrest of the AnN402 germination process enabled CfTer331 to prevent AnN402 from forming mycelia and to gain dominance in the culture. We propose that the collimomycin-dependent arrest of spore germination represents an early intervention strategy used by CfTer331 to mitigate niche construction by fungi in nature.

Green Synthesis of Silver Nanoparticles Using Pseudoduganella eburnea MAHUQ-39 and Their Antimicrobial Mechanisms Investigation against Drug Resistant Human Pathogens.

Silver nanoparticles (AgNPs) have shown great promise in biomedical applications. The exact mechanism and mode of action of AgNPs regarding antimicrobial activity are still not well known. Moreover, synthesis of nanoparticles by physical and chemical methods is expensive and not ecofriendly. This study highlights the green, rapid, facile, cost-effective and ecofriendly synthesis of AgNPs using Pseudoduganella eburnea MAHUQ-39 and also investigates their antibacterial mechanisms. The transmission electron microscopy (TEM) image revealed a spherical shape of the AgNPs. The size of the synthesized AgNPs was 8 to 24 nm. The elemental mapping and selected area electron diffraction (SAED) and X-ray diffraction (XRD) patterns revealed the crystalline structure of AgNPs. Fourier-transform infrared spectroscopy (FTIR) analysis identified the functional groups that are involved in the reduction of silver ion to AgNPs. The green synthesized AgNPs exhibited strong antimicrobial activity against multidrug-resistant pathogenic microbes. Minimal inhibitory concentrations (MICs) of Staphylococcus aureus and Pseudomonas aeruginosa were 100 µg/mL and 6.25 µg/mL, respectively, and the minimum bactericidal concentrations (MBCs) of S. aureus and P. aeruginosa were 200 µg/mL and 50 µg/mL, respectively. Our data demonstrated that synthesized AgNPs created structural changes of cells and destroyed the membrane integrity of strains S. aureus and P. aeruginosa. Therefore, AgNPs synthesized by strain MAHUQ-39 can be used as a powerful antimicrobial agent for various therapeutic applications.

Lacisediminimonas profundi gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from freshwater sediment.

A novel Gram-stain-negative bacterial strain, CHu64-6-4T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu64-6-4T were aerobic nonmotile and formed colorless colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Oxalobacteraceae, exhibiting 97.2% and 97.1% 16S rRNA gene sequence similarities to Glaciimonas singularis and Paraherbaspirillum soli, respectively. Strain CHu64-6-4T showed less than 74.4% average nucleotide identity compared to the type strains of related genera within the family Oxalobacteraceae. In the UPGMA dendrogram based on the ANI values of genomic sequences, strain CHu64-6-4T formed an evolutionary lineage independent of the genera Glaciimonas and some other taxa. The chemotaxonomic results showed Q-8 as the predominant respiratory ubiquinone, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethnolamine as the major polar lipids, Summed Feature 3 (C16:1ω7c and/or iso-C15:0 2-OH), C16:0, and C18:1ω7c as the major fatty acids, and a DNA G+C content of 62.1 mol%. The combined genotypic and phenotypic data showed that strain CHu64-6-4T could be distinguished from all genera within the family Oxalobacteraceae and represents a novel genus, Lacisediminimonas profundi gen. nov., with the name Lacisediminimonas profundi sp. nov., in the family Oxalobacteraceae. The type strain is CHu64-6-4T (=KCTC 62287T=JCM 32676T).

Treatment performance and microbial response to dibutyl phthalate contaminated wastewater in vertical flow constructed wetland mesocosms.

Phthalic acid esters (PAEs), especially dibutyl phthalate (DBP) pollution in the environment, have attracted worldwide attention. Four Phragmites australis-based, mesocosm-scale vertical flow constructed wetlands (VFCWs) with different hydraulic loading rates (HLRs) were operated for one year to study the removal efficiency and mechanisms of DBP in the reclaimed water. The average removal efficiencies for DBP were 93.77 ± 3.27%, 94.9 ± 2.60% and 97.0 ± 3.00% in the VFCWs under HLRs of 0.33, 0.22 and 0.11 m/d, respectively. DBP can be accumulated and degraded by wetland plants and its concentration in the roots (0.256-8.45 mg/kg) were higher than in the leaves (0.243-0.482 mg/kg). The concentrations of primary and secondary metabolites mono-n-butyl phthalate (MBP) and phthalic acid (PA) were 0.142-2.35 mg/kg and 0.113-0.545 mg/kg respectively in the plant tissues. The concentrations of DBP were 38.2-271 µg/kg in the substrates. Mass balance for DBP indicates that the estimated plant uptake and substrate adsorption of total DBP is negligible. This suggests that biodegradation and other process are the primary pathways for DBP removal in VFCWs. The results of 16S rDNA and ITS rDNA high-throughput sequencing indicated that both bacterial and fungal community diversity decreased with the exposure of DBP. Janthinobacterium, Flavobacterium and Curvularia genera may be the main participants in the biodegradation of DBP in the CWs.

Genomic insights revealed physiological diversity and industrial potential for Glaciimonas sp. PCH181 isolated from Satrundi glacier in Pangi-Chamba Himalaya.

Himalayan niches provide unprecedented opportunities for finding novel microbes of commercial importance. The present study investigated the genome sequence of Glaciimonas sp. PCH181 isolated from the glacial stream of Indian trans-Himalaya. The draft genome sequence has six contigs with 5.3 Mb size, 51.1% G + C content, and possesses 4876 genes. Phylogenomic analysis revealed PCH181 as a putative novel bacterium in the genus Glaciimonas. Genomic insight showed Glaciimonas sp. PCH181 enriched with genes for diverse physiology, cold/stress adaptation, and industrial potential. The presence of genes for CO2 fixation and hydrogen metabolism suggested for chemolithoautotrophy. However, genes for sugars and organic acids usage showed heterotrophy and validated by physiological experiments. Genes for the metabolism of phenol (up to 500 ppm) and biosynthesis of polyhydroxyalkanoate (25% of dry cell mass) were also verified. Collectively, we present the first whole genome sequencing in the genus Glaciimonas, a taxonomically, physiologically, and industrially noteworthy bacterium.

Simple or complex organic substrates inhibit arsenite oxidation and aioA gene expression in two ß-Proteobacteria strains.

Microbial transformation of arsenic species and their interaction with the carbon cycle play a major role in the mobility of this toxic metalloid in the environment. The influence of simple or complex organic substrates on arsenic bio-oxidation was studied using two bacterial strains: one - the arsenivorans strain of Thiomonas delicata - is able to use AsIII as sole energy source; the other, Herminiimonas arsenicoxydans, is not. Experiments were performed at two AsIII concentrations (75 and 2 mg/L). At 75 mg/L As, for both strains, expression of aioA gene decreased when yeast extract concentration was raised from 0.2 to 1 g/L. At 2 mg/L As, the presence of either yeast extract or simple (succinate or acetate) organic substrates in the medium during bacterial growth decreased the AsIII-oxidation rate by both strains. When added specifically during oxidation test, yeast extract but not simple organic substrates seems to have a negative effect on AsIII oxidation. Taken together, results confirm the negative influence of simple or complex organic substrates on the kinetics of microbial AsIII oxidation and suggest that this effect results from different mechanisms depending on the type of organic substrate. Further, for the first time, the influence of a complex organic substrate, yeast extract, on aioA gene expression has been evidenced.

Complete genome sequence of Janthinobacterium sp. B9-8, a violacein-producing bacterium isolated from low-temperature sewage.

Janthinobacterium sp. B9-8, isolated from low temperature-sewage in Xinjiang, China, is capable of producing violacein, a promising antibiotic. Here we report the genome sequence of B9-8, which consist of 4,726,850 bp with a G + C content of 48.72%. The violacein biosynthesis gene cluster vioABCDE was identified and analyzed based on the genomic data, which revealed relatively low query coverage (3-44%) and identity (66-87%) with existing strains. Janthinobacterium sp. B9-8 grew fast and reached a high cell density and violacein content within 24 h at 25 °C. The availability of this genome sequence will greatly benefit the industrial production of violacein and facilitate supplementary studies on the mechanism for violacein biosynthesis.

Non-random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer.

Sediments accommodate the dominating share of groundwater microbiomes, however the processes that govern the assembly and succession of sediment-attached microbial communities in groundwater aquifers are not well understood. To elucidate these processes, we followed the microbial colonization of sterile sediments in in situ microcosms that were exposed to groundwater for almost 1 year at two distant but hydrologically connected sites of a pristine, shallow, porous aquifer. Our results revealed intriguing similarities between the community succession on the newly-colonized sediments and succession patterns previously observed for biofilms in other more dynamic aquatic environments, indicating that the assembly of microbial communities on surfaces may be governed by similar underlying mechanisms across a wide range of different habitats. Null model simulations on spatiotemporally resolved 16S rRNA amplicon sequencing data further indicated selection of specific OTUs rather than random colonization as the main driver of community assembly. A small fraction of persistent OTUs that had established on the sediments during the first 115 days dominated the final communities (68%-85%), suggesting a key role of these early-colonizing organisms, in particular specific genera within the Comamonadaceae and Oxalobacteraceae, for community assembly and succession during the colonization of the sediments. Overall, our study suggests that differences between planktonic and sediment-attached communities often reported for groundwater environments are not the result of purely stochastic events, but that sediment surfaces select for specific groups of microorganisms that assemble over time in a reproducible, non-random way.

Investigating the potential use of an Antarctic variant of Janthinobacterium lividum for tackling antimicrobial resistance in a One Health approach.

The aim of this paper is to describe a new variant of Janthinobacterium lividum - ROICE173, isolated from Antarctic snow, and to investigate the antimicrobial effect of the crude bacterial extract against 200 multi-drug resistant (MDR) bacteria of both clinical and environmental origin, displaying various antibiotic resistance patterns. ROICE173 is extremotolerant, grows at high pH (5.5-9.5), in high salinity (3%) and in the presence of different xenobiotic compounds and various antibiotics. The best violacein yield (4.59 ± 0.78 mg·g-1 wet biomass) was obtained at 22 °C, on R2 broth supplemented with 1% glycerol. When the crude extract was tested for antimicrobial activity, a clear bactericidal effect was observed on 79 strains (40%), a bacteriostatic effect on 25 strains (12%) and no effect in the case of 96 strains (48%). A very good inhibitory effect was noticed against numerous MRSA, MSSA, Enterococci, and Enterobacteriaceae isolates. For several environmental E. coli strains, the bactericidal effect was encountered at a violacein concentration below of what was previously reported. A different effect (bacteriostatic vs. bactericidal) was observed in the case of Enterobacteriaceae isolated from raw vs. treated wastewater, suggesting that the wastewater treatment process may influence the susceptibility of MDR bacteria to violacein containing bacterial extracts.

Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community.

Although bioaugmentation of pollutant-contaminated sites is a great concern, there are few reports on the relationships among indigenous microbial consortia, exogenous inocula, and pollutants in a bioaugmentation process. In this study, bioaugmentation with Pseudochrobactrum sp. BSQ1 and Massilia sp. BLM18, which can hydrolytically and reductively dehalogenate chlorothalonil (TPN), respectively, was studied for its ability to remove TPN from soil; the alteration of the soil microbial community during the bioaugmentation process was investigated. The results showed that TPN (50 mg/kg) was completely removed in both bioaugmentation treatments within 35 days with half-lives of 6.8 and 9.8 days for strains BSQ1 and BLM18 respectively. In high concentration of TPN-treated soils (100 mg/kg), the bioaugmentation with strains BSQ1 and BLM18 respectively reduced 76.7% and 62.0% of TPN within 35 days. The TPN treatment significantly decreased bacterial richness and diversity and improved the growth of bacteria related to the elimination of chlorinated organic pollutants. However, little influence on soil microbial community was observed for each inoculation treatment (without TPN treatment), showing that TPN treatment is the main force for the shift in indigenous consortia. This study provides insights into the effects of halogenated fungicide application and bioaugmentation on indigenous soil microbiomes.