Keguizhuia sedimenti gen. nov., sp. nov., isolated from river sediment represents a novel genus of the family Oxalobacteraceae.

A Gram-stain-negative bacterium, designated as R-40T, was isolated from sediment of the Mulong river in Mianyang city, Sichuan province, PR China. The cells of strain R-40T were aerobic non-motile and formed translucent white colonies on R2A agar. Growth occurred at 15-37 °C (optimum 30 °C), pH 5.0-9.0 (optimum 7.0) and salinities of 0-3.0 % (w/v, optimum 0 %). R-40T showed 95.2-96.6 % 16S rRNA gene sequence similarities with the type strains of species of the genera Oxalicibacterium, Herminiimonas, Lacisediminimonas, Paucimonas, Herbaspirillum and Noviherbaspirillum in the family Oxalobacteraceae. The results of phylogenetic analysis based on genome sequences indicated that the strain was clustered with type strains of species of the genera Oxalicibacterium and Herminiimonas in the family Oxalobacteraceae but formed a distinct lineage. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between R-40T and type strains of species of the genera Oxalicibacterium, Herminiimonas, Lacisediminimonas, Paucimonas, Herbaspirillum and Noviherbaspirillum ranged from 69.3 to 74.1 %, from 18.2 to 21.4 % and from 60.1 to 67.4 %, respectively. The major cellular fatty acids were C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major quinone was ubiquinone-8 (Q-8). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and small amounts of glycophospholipids. The genome size of R-40T was 5.1 Mbp with 54.0 % DNA G+C content. On the basis of the evidence presented in this study, strain R-40T represents a novel species of a novel genus in the family Oxalobacteraceae, for which the name Keguizhuia sedimenti gen. nov., sp. nov. (type strain R-40T=MCCC 1K08818T=KCTC 8137T) is proposed.

Functional characterization of the methylarsenite-inducible arsRM operon from Noviherbaspirillum denitrificans HC18.

Microbial arsenic methylation by arsenite (As(III)) S-adenosylmethionine methyltransferases (ArsMs) can produce the intermediate methylarsenite (MAs(III)), which is highly toxic and is used by some microbes as an antibiotic. Other microbes have evolved mechanisms to detoxify MAs(III). In this study, an arsRM operon was identified in the genome of an MAs(III)-methylation strain Noviherbaspirillum denitrificans HC18. The arsM gene (NdarsM) is located downstream of an open reading frame encoding an MAs(III)-responsive transcriptional regulator (NdArsR). The N. denitrificans arsRM genes are co-transcribed whose expression is significantly induced by MAs(III), likely by alleviating the repressive effect of ArsR on arsRM transcription. Both in vivo and in vitro assays showed that NdArsM methylates MAs(III) to dimethyl- and trimethyl-arsenicals but does not methylate As(III). Heterologous expression of NdarsM in arsenic-sensitive Escherichia coli AW3110 conferred resistance to MAs(III) but not As(III). NdArsM has the four conserved cysteine residues present in most ArsMs, but only two of them are essential for MAs(III) methylation. The ability to methylate MAs(III) by enzymes such as NdArsM may be an evolutionary step originated from enzymes capable of methylating As(III). This finding reveals a mechanism employed by microbes such as N. denitrificans HC18 to detoxify MAs(III) by further methylation.

Functional characterization of a novel violacein biosynthesis operon from Janthinobacterium sp. B9-8.

Violacein is a secondary metabolite mainly produced by Gram-negative bacteria that is formed from tryptophan by five enzymes encoded by a single operon. It is a broad-spectrum antibacterial pigment with various important biological activities such as anti-tumor, antiviral, and antioxidative effects. The newly discovered violacein operon vioABCDE was identified in the genome of the extremophile Janthinobacterium sp. B9-8. The key enzyme-encoding genes were cloned to construct the multigene coexpression plasmids pET-vioAB and pRSF-vioCDE. The violacein biosynthesis pathway was heterologously introduced into engineered Escherichia coli VioABCDE and VioABCDE-SD. The factors affecting violacein production, including temperature, pH, inoculum size, carbon and nitrogen source, precursor, and inducers were investigated. The violacein titer of VioABCDE-SD reached 107 mg/L in a two-stage fermentation process, representing a 454.4% increase over the original strain. The violacein operon from B9-8 provides a new microbial gene source for the analysis of the violacein synthesis mechanism, and the constructed engineering E. coli strains lay a foundation for the efficient and rapid synthesis of other natural products.Key points• The newly discovered violacein operon vioABCDE was identified in the genome of the extremophile Janthinobacterium sp. B9-8.• The violacein synthesis pathway was reconstructed in E. coli using two compatible plasmids.• A two-stage fermentation process was optimized for improved violacein accumulation.

Genome Analysis of the Janthinobacterium sp. Strain SLB01 from the Diseased Sponge of the Lubomirskia baicalensis.

The strain Janthinobacterium sp. SLB01 was isolated from the diseased freshwater sponge Lubomirskia baicalensis (Pallas, 1776) and the draft genome was published previously. The aim of this work is to analyze the genome of the Janthinobacterium sp. SLB01 to search for pathogenicity factors for Baikal sponges. We performed genomic analysis to determine virulence factors, comparing the genome of the strain SLB01 with genomes of other related J. lividum strains from the environment. The strain Janthinobacterium sp. SLB01 contained genes encoding violacein, alpha-amylases, phospholipases, chitinases, collagenases, hemolysin, and a type VI secretion system. In addition, the presence of conservative clusters of genes for the biosynthesis of secondary metabolites of tropodithietic acid and marinocine was found. We present genes for antibiotic resistance, including five genes encoding various lactamases and eight genes for penicillin-binding proteins, which are conserved in all analyzed strains. Major differences were found between the Janthinobacterium sp. SLB01 and J. lividum strains in the spectra of genes for glycosyltransferases and glycoside hydrolases, serine hydrolases, and trypsin-like peptidase, as well as some TonB-dependent siderophore receptors. Thus, the study of the analysis of the genome of the strain SLB01 allows us to conclude that the strain may be one of the pathogens of freshwater sponges.

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.

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.

Noviherbaspirillum galbum sp. nov., a bacterium isolated from soil.

A Gram-stain-negative, aerobic, non-motile and yellow-colored bacterium, strain 17J57-3 T, was isolated from soil collected in Pyeongchang city, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 17J57-3 T formed a distinct lineage within the family Oxalobacteraceae (order Burkholderiales, class Betaproteobacteria). Strain 17J57-3 T was the most closely related to Noviherbaspirillum humi U15T (96.4% 16S rRNA gene sequence similarity) and Noviherbaspirillum massiliense JC206T (96.2%). The draft genome size of strain 17J57-3 T was 6,117,206 bp. Optimal growth occurred at 30 °C, pH 7.0 without NaCl. The predominant cellular fatty acids were summed feature 3 (C16:1 ω6c/C16:1 ω7c) and C16:0. The major respiratory quinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strain 17J57-3 T represents a novel bacterial species within the genus Noviherbaspirillum, for which the name Noviherbaspirillum galbum is proposed. The type strain of Noviherbaspirillum galbum is 17J57-3 T (= KCTC 62213 T = NBRC 114384 T).

Noviherbaspirillum pedocola sp. nov., isolated from oil-contaminated experimental soil.

An orange-coloured, rod-shaped, and aerobic bacterial strain DKR-6 T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10-42 °C, at pH 5.5-9.5, and at 0-3.0% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-6 T was affiliated to the genus Noviherbaspirillum, with the closest species being Noviherbaspirillum massiliense JC206T (96.3% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine as the principal polar lipids; C16:0, C17:0 cyclo, summed feature 3 (C16:1ω7c and/or C16: 1ω6c), and summed feature 8 (C18:1ω7c/or C18:1ω6c) as the main fatty acids; and Q-8 as a sole ubiquinone. The DNA G + C content was 61.6%. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-6 T represents a novel species in the genus Noviherbaspirillum, for which the name Noviherbaspirillum pedocola sp. nov. is proposed with the type strain DKR-6 T (= KACC 22074 T = NBRC 114727 T).

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.

Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation.

A straw coloured, motile and Gram-stain-negative bacterium, designated RP-1-19T was isolated from soil of Arctic station, Svalbard, Norway. Based on the phylogenetic analysis of its 16S rRNA gene sequence, strain RP-1-19T formed a lineage within the family Oxalobacteraceae and clustered together within the genus Massilia. The closest members were M. violaceinigra B2T (98.6% sequence similarity), M. eurypsychrophilia JCM 30074T (98.3%) and M. atriviolacea SODT (98.1%). The only respiratory quinone was ubiquinone-8. The principal cellular fatty acids were summed feature 3 (iso-C15:0 2-OH/C16:1ω7c) and C16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain was 63.2%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RP-1-19T and closest members were ≤ 80 and 23.2%, respectively. The genome was 4,522,469 bp long with 30 scaffolds and 4076 protein-coding genes. The genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome analysis revealed the presence of cold-shock proteins CspA and CspC. Presence of cspA and cspC genes in the genome manifest ecophysiology of strain RP-1-19T that may help in cold-adaptation. Based on these data, strain RP-1-19T represents a novel species in the genus Massilia, for which the name Massilia polaris sp. nov. is proposed. The type strain is RP-1-19T (= KACC 21619T = NBRC 114359T).

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.

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.

Glaciimonas soli sp. nov., a soil bacterium isolated from the forest of a high elevation mountain.

A Gram-negative, psychrophilic bacterium, designated strain GS1T, was isolated from a forest soil sample collected from the West Peak of Mt. Yushan, Yushan National Park, Taiwan. Cells grown in broth cultures were mostly non-motile and non-flagellated, whereas motile cells with monotrichous, subpolar flagella were also observed. The novel strain grew over a temperature range of 4-25 °C with optimum growth at 10-15 °C. It grew aerobically and was not capable of anaerobic growth by fermentation of D-glucose or other carbohydrates. Ubiquinone 8 was the predominant isoprenoid quinone. The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol and dimethylaminoethanol. Cellular fatty acids were dominated by C16:1ω7c (35.2%), C16:0 (19.5%), C18:1ω7c (18.8%) and C17:0ω7c cyclo (15.5%). The DNA G + C content was 49.2 mol% evaluated according to the genomic sequencing data. Strain GS1T shared more than 96.5% 16S rRNA gene sequence similarities with type strains of four Collimonas species (97.2-97.5%), three Glaciimonas species (97.3% for each of the three) and Oxalicibacterium solurbis (96.5%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GS1T formed a stable genus-level clade with type strains of species in the genus Glaciimonas in the family Oxalobacteraceae and GS1T was an outgroup with respect to these Glaciimonas species. Characteristically, strain GS1T could be easily distinguished from the recognised Glaciimonas species by exhibition of swimming motility with monotrichous, subpolar flagellum in some of the cells, ability to grow in NaCl at 2% but not at 3% and the distinguishable fatty acid profiles. On the basis of the polyphasic taxonomic data from this study, strain GS1T is considered to represent a novel species of the genus Glaciimonas, for which the name Glaciimonas soli sp. nov. is proposed. The type strain is GS1T (= JCM 33275T = BCRC 81091T).

Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella.

Four Gram-stain-negative, catalase-positive, rod-shaped and motile strains (FT55WT, FT93WT, CY13WT and DS3T) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences indicated that strains FT55WT, FT93WT and CY13WT take strain Pseudoduganella danionis E3/2T, and strain DS3T takes strain Pseudoduganella eburnea 10R5-21T as their closest neighbour, respectively. The genome sizes of strains FT55WT, FT93WT, CY13WT and DS3T were 6.15, 5.10, 5.31 and 5.72 Mbp with G+C contents of 61.7, 60.9, 60.6 and 64.0%, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strain FT55WT clusters closely with Duganella radicis KCTC 22382T and Duganella sacchari Sac-22T, strains FT93WT and CY13WT form a distinct clade with P. danionis DSM 103461T and this clade clusters with the clades of genus Duganella together, and strain DS3T forms a distinct clade with P. eburnea JCM 31587T and Pseudoduganella violaceinigra DSM 15887T and this clade clusters closely with the clades of genus Massilia, respectively. The calculated pairwise OrthoANIu values and digital DNA-DNA hybridization (DDH) values among strains FT55WT, FT93WT, CY13WT, DS3T and related strains were in the ranges of 75.6-94.2% and 20.6-56.2%, respectively. Q-8 was the sole respiratory quinone of these four strains. The major fatty acids were C16:1ω7c, C16:0 and C12:0. The polar lipids included phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. Considering the similar fatty acids and polar lipids profiles of species within genus Pseudoduganella, Massilia and Duganella, there is currently no justification for assigning the species of genus Pseudoduganella into the Massilia and Duganella clades in the phylogenomic tree. It is reasonable to transfer P. violaceinigra and P. eburnea to the genus Massilia as Massilia violaceinigrum comb. nov. and Massilia eburnea comb. nov., and transfer P. danionis to the genus Duganella as Duganella danionis comb. nov. Considering phylogenomic analysis, OrthoANIu data, digital DDH data and a range of physiological and biochemical characteristics, strains FT55WT, FT93WT and CY13WT should be assigned to genus Duganella, and strain DS3T should be classified as a novel species within genus Massilia, for which the names Duganella rivus sp. nov. (type strain FT55WT = GDMCC 1.1675T = KACC 21467T), Duganella fentianensis sp. nov. (type strain FT93WT = GDMCC 1.1683T = KACC 21475T), Duganella qianjiadongensis sp. nov. (type strain CY13WT = GDMCC 1.1669T = KACC 21461T) and Massilia guangdongensis sp. nov. (type strain DS3T = GDMCC 1.1636T = KACC 21312T) are proposed.

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).

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.

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.

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.

Recombinant expression, purification, and characterization of a cyclodextrinase from Massilia timonae.

Some microorganisms can produce cyclodextrin glycosyltransferases, which degrades starch by catalyzing cyclization and giving rise to cyclodextrin. Thus, to fully degrade starch, microorganisms can also synthesize cyclodextrinases, which hydrolyze cyclodextrins. In this work, a truncated gene, without the signal peptide coding sequence, encoding a cyclodextrinase from Massilia timonae was PCR amplified, cloned, and expressed in E. coli. The histidine-tagged recombinant enzyme was purified by immobilized metal ion affinity chromatography. The purified protein was found to be a tetramer of about 260 kDa, with monomers of about 65 kDa, as estimated by gel filtration and SDS-PAGE, respectively. The enzyme presented an optimum temperature of 40 °C, optimum pH of 7.0, and remained stable after 30 min of incubation at 45 °C, with a T50 of 48.45 °C. The enzyme showed a higher activity toward ß-cyclodextrin compared to that for maltodextrin and starch. KM for ß-cyclodextrin was 2.1 mM, Vmax was 0.084 µmol/min, kcat was 8326 min-1, and kcat/KM was 4.1 × 106 M-1min-1. Calcium acted as an activator and SDS, CTAB, several cations, and EDTA acted as strong inhibitors. The purified cyclodextrinase produced glucose and maltose as final products by hydrolysis of ß-cyclodextrin, maltotetraose, and maltoheptaose. This novel cyclodextrinase could be a promising alternative for the enzymatic hydrolysis of starch.

A new cold-active and alkaline pectate lyase from Antarctic bacterium with high catalytic efficiency.

Cold-active enzymes have become attractive biocatalysts in biotechnological applications for their ability to retain high catalytic activity below 30 °C, which allows energy reduction and cost saving. Here, a 1041 bp gene pel1 encoding a 34.7 KDa pectate lyase was cloned from a facultatively psychrophilic Antarctic bacterium Massilia eurypsychrophila and heterologously expressed in Escherichia coli. PEL1 presented the highest 66% identity to the reported mesophilic pectate lyase PLXc. The purified PEL1 exhibits the optimum temperature and pH of 30 °C and 10 toward polygalacturonic acid, respectively. PEL1 is a cold-active enzyme that can retain 60% and 25% relative activity at 10 °C and 0 °C, respectively, while it loses most of activity at 40 °C for 10 min. PEL1 has the highest specific activity (78.75 U mg-1) than all other reported cold-active pectinase, making it a better choice for use in industry. Based on the detailed sequence and structure comparison between PEL1 and PLXc and mutation analysis, more flexible structure and some loop regions may contribute to the cold activity and thermal instability of PEL1. Our investigations of the cold-active mechanism of PEL1 might guide the rational design of PEL1 and other related enzymes.