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Extremophiles : Life Under Extreme... Nov 2022The current study describes a novel species with the strain name ERMR1:05 isolated from the forefield soil of East Rathong Glacier in West Sikkim Himalaya (India). The...
The current study describes a novel species with the strain name ERMR1:05 isolated from the forefield soil of East Rathong Glacier in West Sikkim Himalaya (India). The isolate was facultatively anaerobic, gram-stain negative, non-spore-forming, rod-shaped, and oxidase negative. Whole-genome-based bacterial core gene phylogenetic analysis placed the strain in the genus Rahnella, well separated from Rouxiella spp. The digital DNA-DNA hybridisation and average nucleotide identity values between strain ERMR1:05 and other members of genus Rahnella were below the proposed thresholds for the species delineation. Based on these results, a new species, Rahnella sikkimica sp. nov., is proposed with strain ERMR1:05 (CIP 111636, MTCC 12598) as the type strain. The bacterium showed upregulation of cold-stress genes in cold conditions. Additionally, the genome analysis of the bacterium showed the presence of plant growth-promotion factors suggesting its role in crop improvement in cold hilly regions.
Topics: Ice Cover; Rahnella; RNA, Ribosomal, 16S; Phylogeny; DNA, Bacterial; Bacterial Typing Techniques; Base Composition; Sikkim; Sequence Analysis, DNA; Fatty Acids; Phospholipids
PubMed: 36378360
DOI: 10.1007/s00792-022-01283-y -
International Journal of Molecular... Apr 2021There has been a recent increase in the exploration of cold-active β-galactosidases, as it offers new alternatives for the dairy industry, mainly in response to the...
There has been a recent increase in the exploration of cold-active β-galactosidases, as it offers new alternatives for the dairy industry, mainly in response to the current needs of lactose-intolerant consumers. Since extremophilic microbial compounds might have unique physical and chemical properties, this research aimed to study the capacity of Antarctic bacterial strains to produce cold-active β-galactosidases. A screening revealed 81 out of 304 strains with β-galactosidase activity. The strain Se8.10.12 showed the highest enzymatic activity. Morphological, biochemical, and molecular characterization based on whole-genome sequencing confirmed it as the first isolate from the Antarctic, which retained 41-62% of its β-galactosidase activity in the cold (4 °C-15 °C). Three β-galactosidases genes were found in the genome, which belong to the glycoside hydrolase families GH2 (LacZ and EbgA) and GH42 (BglY). Based on molecular docking, some of these enzymes exhibited higher lactose predicted affinity than the commercial control enzyme from . Hence, this work reports a new strain from the Antarctic continent as a prominent cold-active β-galactosidase producer.
Topics: Acclimatization; Cold Temperature; Enzyme Stability; Rahnella; beta-Galactosidase
PubMed: 33923711
DOI: 10.3390/ijms22084144 -
Diagnostic Microbiology and Infectious... Jul 1995Rahnella aquatilis, an unusual enteric Gram-negative rod, was isolated from three of four blood cultures of an HIV-infected intravenous drug abuser. The outcome was... (Review)
Review
Rahnella aquatilis, an unusual enteric Gram-negative rod, was isolated from three of four blood cultures of an HIV-infected intravenous drug abuser. The outcome was favorable after a 14-day course with ciprofloxacin. The identification of R. aquatilis isolates is discussed and a synopsis of the previously published antimicrobial susceptibility patterns of this microorganism is given.
Topics: Acquired Immunodeficiency Syndrome; Adult; Anti-Infective Agents; Bacteremia; Ciprofloxacin; Gram-Negative Anaerobic Bacteria; Gram-Negative Bacterial Infections; Humans; Male; Microbial Sensitivity Tests; Substance Abuse, Intravenous
PubMed: 8565419
DOI: 10.1016/0732-8893(95)00100-o -
Archives of Microbiology Nov 2020A Gram-reaction-negative, facultatively anaerobic bacterium, designated SAP-19, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea...
A Gram-reaction-negative, facultatively anaerobic bacterium, designated SAP-19, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its taxonomic statue was investigated by a polyphasic approach including genome- and 16S rRNA gene-based phylogenetic analyses. Cells were motile, short rods and showed growth at 20-30 °C, pH 4-9 and 0-6% (w/v) NaCl. The whole genome- and 16S rRNA gene-based phylogenetic analyses exhibited that strain SAP-19 belongs to the genus Rahnella and forms a tight cluster with Rahnella aquatilis. The isolate shared average nucleotide identity of 92.7% and 16S rRNA gene sequence similarity of 99.6% with the type strain of Rahnella aquatilis. The polar lipids contained phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The major isoprenoid quinone was Q-8. The predominant fatty acids were C and Ccyclo. The G + C content of the genome was 52.3%. The low average nucleotide identity (92.7%) and digital DNA relatedness (48.6%) values between the isolate and the most closely related strain showed that the isolate can be considered a different genospecies. On the basis of combined data obtained in this study, strain SAP-19 (= KACC 21744 = NBRC 114407) represents a novel species of the genus Rahnella, for which the name Rahnella aceris sp. nov. is proposed.
Topics: Acer; Bacterial Typing Techniques; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Rahnella; Republic of Korea; Species Specificity
PubMed: 32591910
DOI: 10.1007/s00203-020-01961-5 -
Frontiers in Microbiology 2022sp. ChDrAdgB13 is a dominant member of the gut bacterial core of species of the genus , which is one of the most destructive pine forest bark beetles. The objectives of...
sp. ChDrAdgB13 is a dominant member of the gut bacterial core of species of the genus , which is one of the most destructive pine forest bark beetles. The objectives of this study were identified in sp. ChDrAdgB13 genome the glycosyl hydrolase families involved in carbohydrate metabolism and specifically, the genes that participate in xylan hydrolysis, to determine the functionality of a putative -1,4-β-D-xylanase, which results to be bifunctional xylanase-ferulic acid esterase called R13 Fae and characterize it biochemically. The carbohydrate-active enzyme prediction revealed 25 glycoside hydrolases, 20 glycosyl transferases, carbohydrate esterases, two auxiliary activities, one polysaccharide lyase, and one carbohydrate-binding module (CBM). The R13 Fae predicted showed high identity to the putative esterases and glycosyl hydrolases from species and some members of the Yersiniaceae family. The gene encodes 393 amino acids (43.5 kDa), containing a signal peptide, esterase catalytic domain, and CBM48. The R13 Fae modeling showed a higher binding affinity to ferulic acid, α-naphthyl acetate, and arabinoxylan, and a low affinity to starch. The R13 Fae recombinant protein showed activity on α-naphthyl acetate and xylan, but not on starch. This enzyme showed mesophilic characteristics, displaying its optimal activity at pH 6.0 and 25°C. The enzyme was stable at pH from 4.5 to 9.0, retaining nearly 66-71% of its original activity. The half-life of the enzyme was 23 days at 25°C. The enzyme was stable in the presence of metallic ions, except for Hg. The products of R13 Fae mediated hydrolysis of beechwood xylan were xylobiose and xylose, manifesting an -activity. The results suggest that sp. ChDrAdgB13 hydrolyze xylan and its products could be assimilated by its host and other gut microbes as a nutritional source, demonstrating their functional role in the bacterial-insect interaction contributing to their fitness, development, and survival.
PubMed: 35711755
DOI: 10.3389/fmicb.2022.911269 -
Frontiers in Plant Science 2022Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have...
Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in , and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography-mass spectrometry (LC-MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of , which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the rhizosphere soil and increased the abundances of specific taxa, such as , , and . Therefore, JZ-GX1 application promoted iron absorption in trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.
PubMed: 36186024
DOI: 10.3389/fpls.2022.960750 -
Journal of Applied Microbiology Sep 2019Bacterial decays of onion bulbs have serious economic consequences for growers, but the aetiologies of these diseases are often unclear. We aimed to determine the role...
AIMS
Bacterial decays of onion bulbs have serious economic consequences for growers, but the aetiologies of these diseases are often unclear. We aimed to determine the role of Rahnella, which we commonly isolated from bulbs in the United States and Norway, in onion disease.
METHODS AND RESULTS
Isolated bacteria were identified by sequencing of housekeeping genes and/or fatty acid methyl ester analysis. A subset of Rahnella spp. strains was also assessed by multilocus sequence analysis (MLSA); most onion strains belonged to two clades that appear closely related to R. aquatilis. All tested strains from both countries caused mild symptoms in onion bulbs but not leaves. Polymerase chain reaction primers were designed and tested against strains from known species of Rahnella. Amplicons were produced from strains of R. aquatilis, R. victoriana, R. variigena, R. inusitata and R. bruchi, and from one of the two strains of R. woolbedingensis.
CONCLUSIONS
Based on binational testing, strains of Rahnella are commonly associated with onions, and they are capable of causing mild symptoms in bulbs.
SIGNIFICANCE AND IMPACT OF THE STUDY
While Rahnella strains are commonly found within field-grown onions and they are able to cause mild symptoms, the economic impact of Rahnella-associated symptoms remains unclear.
Topics: Genes, Essential; New York; Norway; Onions; Phylogeny; Plant Diseases; Plant Leaves; Plant Roots; Polymerase Chain Reaction; Rahnella
PubMed: 31161611
DOI: 10.1111/jam.14340 -
Scandinavian Journal of Infectious... 2001Rahnella aquatilis infections are rare. We report the case of a 46-y-old African-American male with relapsed acute lymphoblastic leukemia who had R. aquatilis bacteremia... (Review)
Review
Rahnella aquatilis infections are rare. We report the case of a 46-y-old African-American male with relapsed acute lymphoblastic leukemia who had R. aquatilis bacteremia after beginning reinduction chemotherapy. He was treated for 4 weeks with piperacillin-tazobactam and gentamicin. He recovered from the infection and had an allogenic bone marrow transplant a month later.
Topics: Bacteremia; Bone Marrow Transplantation; Burkitt Lymphoma; Drug Therapy, Combination; Gram-Negative Bacterial Infections; Humans; Immunocompromised Host; Immunosuppressive Agents; Male; Middle Aged; Penicillanic Acid; Piperacillin; Piperacillin, Tazobactam Drug Combination; Rahnella
PubMed: 11450870
DOI: 10.1080/00365540152029972 -
International Journal of Systematic and... Jan 2022Bacteria isolated from onion bulbs suffering from bacterial decay in the United States and Norway were previously shown to belong to the genus based on partial...
Bacteria isolated from onion bulbs suffering from bacterial decay in the United States and Norway were previously shown to belong to the genus based on partial housekeeping gene sequences and/or fatty acid analysis. However, many strains could not be assigned to any existing species. Additionally, strains isolated from creek water and oak as well as a strain with bioremediation properties were assigned to based on partial housekeeping gene sequences. The taxonomic status of these 21 strains was investigated using multilocus sequence analysis, whole genome analyses, phenotypic assays and fatty acid analysis. Phylogenetic and phylogenomic analyses separated the strains into five clusters, one of which corresponded to . The remaining four clusters could be differentiated both genotypically and phenotypically from each other and existing species. Based on these results, we propose the description of four novel species: sp. nov. (type strain SL6=LMG 32257=DSM 112609), sp. nov. (H11b=LMG 32256=DSM 112610), sp. nov. (FC061912-K=LMG 32259=DSM 112611) and sp. nov. (FRB 231=LMG 32255=DSM 112612).
Topics: Bacterial Typing Techniques; DNA, Bacterial; Multilocus Sequence Typing; Onions; Phylogeny; Quercus; RNA, Ribosomal, 16S; Rahnella; Rivers; Sequence Analysis, DNA
PubMed: 35133259
DOI: 10.1099/ijsem.0.005190 -
International Journal of Systematic and... Jul 2021Taxonomic positions of six isolates, which were recovered from two different environments in Jeju, Republic of Korea, were examined by a polyphasic analysis. Cells of...
Taxonomic positions of six isolates, which were recovered from two different environments in Jeju, Republic of Korea, were examined by a polyphasic analysis. Cells of the isolates were Gram-reaction-negative, facultatively anaerobic, motile and rod-shaped and showed growth at 4-30 °C, pH 4.0-9.0 and with 0-6 (w/v) NaCl. In phylogenomic analysis based on 92 single-copy core genes, it was shown that the isolates belonged to the genus and formed three distinct sublines within the genus. The isolates shared 16S rRNA gene sequence similarities of 97.9-100 % with one another. The isolates contained ubiquinone-8 was as the major isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were C and C cyclo. The G+C content of their genomic DNA was 52.8-53.1 %. Average nucleotide identity and digital DNA-DNA hybridization values supported that strains SAP-17 and Lac-M11 represented two new species of the genus , whereas strain SAP-10 was a strain of . Based on the results obtained here, sp. nov. (type strain SAP-17=KCTC 72960=NBRC 114723=CCM 9079) and sp. nov. (type strain Lac-M11=KACC 21743=NBRC 114406) are proposed. Also, an emended description of the genus is given on the basis of our physiological and chemotaxonomic results.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Rahnella; Republic of Korea; Sequence Analysis, DNA; Ubiquinone
PubMed: 34214024
DOI: 10.1099/ijsem.0.004893