scholarly journals Strain IMB-1, a Novel Bacterium for the Removal of Methyl Bromide in Fumigated Agricultural Soils

1998 ◽  
Vol 64 (8) ◽  
pp. 2899-2905 ◽  
Author(s):  
Tracy L. Connell Hancock ◽  
Andria M. Costello ◽  
Mary E. Lidstrom ◽  
Ronald S. Oremland
Keyword(s):  
Methyl Iodide ◽  
Methyl Bromide ◽  
Agricultural Soils ◽  
Treatment Strategies ◽  
Methyl Chloride ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Low Concentrations ◽  
Novel Bacterium ◽  
Bacterium Strain

ABSTRACT A facultatively methylotrophic bacterium, strain IMB-1, that has been isolated from agricultural soil grows on methyl bromide (MeBr), methyl iodide, methyl chloride, and methylated amines, as well as on glucose, pyruvate, or acetate. Phylogenetic analysis of its 16S rRNA gene sequence indicates that strain IMB-1 classes in the alpha subgroup of the class Proteobacteria and is closely related to members of the genus Rhizobium. The ability of strain IMB-1 to oxidize MeBr to CO2 is constitutive in cells regardless of the growth substrate. Addition of cell suspensions of strain IMB-1 to soils greatly accelerates the oxidation of MeBr, as does pretreatment of soils with low concentrations of methyl iodide. These results suggest that soil treatment strategies can be devised whereby bacteria can effectively consume MeBr during field fumigations, which would diminish or eliminate the outward flux of MeBr to the atmosphere.

Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1647-1652 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin ◽  
Kazuhide Kimbara
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
Sequence Similarities

A pink-pigmented, facultatively methylotrophic bacterium, strain 35aT, was isolated from the leaves of Oxalis corniculata. Cells of strain 35aT were Gram-reaction-negative, motile, non-spore-forming rods. The highest 16S rRNA gene pairwise sequence similarities for strain 35aT were found with the strains of Methylobacterium iners 5317S-33T (96.7 %), ‘Methylobacterium soli’ YIM 48816 (96.6 %) and Methylobacterium jeotgali S2R03-9T (96.3 %). 16S rRNA gene sequence similarities with the type strains of all other recognized species of the genus Methylobacterium were below 96 %. Major cellular fatty acids were C18 : 1ω7c, C18 : 0 and C16 : 0. The results of DNA–DNA hybridization experiments, analysis of cpn60 gene sequences, fatty acid profiles, whole-cell MALDI-TOF/MS spectral pattern analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 35aT from its nearest phylogenetic neighbours. Strain 35aT is therefore considered to represent a novel species within the genus Methylobacterium , for which the name Methylobacterium oxalidis sp. nov. is proposed. The type strain is 35aT ( = DSM 24028T = NBRC 107715T).

Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2602-2607 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin ◽  
Kazuhide Kimbara
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Cell Matrix ◽  
Bacterium Strain

A pink-pigmented, facultatively methylotrophic bacterium, strain 23eT, was isolated from the leaves of Gnaphalium spicatum (cudweed). The cells of strain 23eT were Gram-reaction negative, motile and non-spore-forming rods. On the basis of 16S rRNA gene sequence similarities, strain 23eT was related to Methylobacterium organophilum ATCC 27886T (97.1 %) and Methylobacterium marchantiae JT1T (97 %), and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 97 %. Major cellular fatty acids were C18 : 1ω7c, C16 : 00 and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted laser desorption/ionization time of flight/MS analysis, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 23eT from the phylogenetically closest relatives. We propose that strain 23eT represents a novel species within the genus Methylobacterium , for which the name Methylobacterium gnaphalii sp. nov. is proposed. The type strain is 23eT ( = DSM 24027T = NBRC 107716T).

Xanthobacter oligotrophicus sp.nov., isolated from paper mill sewage

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ekaterina N. Tikhonova ◽  
Denis S. Grouzdev ◽  
Irina K. Kravchenko
Keyword(s):  
Type Species ◽  
Paper Mill ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Bacterium Strain

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29kT, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5–0.7×1.7–3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C18:1 ω7, C19:0 cyclo and C16:0. The genomic DNA G+C content was 67.95 mol%. Strain 29kT was able to grow at 4–37 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 6.5–7.0) and at salinities of 0–0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29kT could grow chemolithoautotrophically in mineral media under an atmosphere of H2, O2 and CO2 as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Xanthobacter with Xanthobacter autotrophicus 7cT (99.9% similarity) and Xanthobacter viscosus 7dT (99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA–DNA hybridization values of 92.7 and 44.9%, respectively, of the 29kT to the genome of the most closely related species, X. autotrophicus 7cT, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Xanthobacter oligotrophicus sp. nov. The type strain is 29kT (=KCTC 72777T=VKM B-3453T).

Methyloversatilis thermotolerans sp. nov., a novel thermotolerant facultative methylotroph isolated from a hot spring

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 158-164 ◽  
Author(s):  
Nina V. Doronina ◽  
Elena N. Kaparullina ◽  
Yuri A. Trotsenko
Keyword(s):  
Type Species ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A newly isolated facultatively methylotrophic bacterium (strain 3tT) was investigated. Cells of the isolate were Gram-stain-negative, asporogenous, non-motile rods that multiplied by binary fission. The strain utilized methanol, methylamine and a variety of multicarbon compounds as carbon and energy sources. Growth occurred at pH 6.5–8.5 (optimally at 7.0–7.5) and at 10–45 °C (optimally at 30–37 °C). The major fatty acids of methanol-grown cells were C16 : 1ω7c and C16 : 0. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. Strain 3tT possessed pyrroloquinoline quinone (PQQ)-linked methanol dehydrogenase and assimilated C1 units at the level of formaldehyde and CO2 via the serine cycle. The DNA G+C content of the strain was 63.6 mol% (T m). On the basis of 16S rRNA gene sequence similarity (98.1 %) and rather low DNA–DNA relatedness (30 %) with the type strain of the type species of the genus Methyloversatilis ( Methyloversatilis universalis FAM5T), and physiological and biochemical characteristics, the isolate was classified as a representative of a new species of the genus and named Methyloversatilis thermotolerans 3tT ( = VKM B-2692T = CCUG 61694T = DSM 25156T).

scholarly journals Formosa sediminum sp. nov., a starch-degrading bacterium isolated from marine sediment

2020 ◽  
Vol 70 (3) ◽  
pp. 2008-2015 ◽  
Author(s):  
Bit Han ◽  
Minji Kim ◽  
Ki-Eun Lee ◽  
Byoung-Hee Lee ◽  
Eun-Young Lee ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Novel Bacterium ◽  
Bacterium Strain

A novel bacterium, designated strain PS13T, was isolated from marine sediment collected from the coast of Jeju Island. Strain PS13T was a Gram stain-negative, catalase- and oxidase-positive, aerobic, yellow-pigmented, motile by gliding, and rod-shaped bacterium. Strain PS13T grew optimally at 25 °C and pH 8.0 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain PS13T belonged to the genus Formosa and was closely related to Formosa algae KMM3553T (98.3 % sequence similarity). The DNA–DNA relatedness (17.3–21.8 %) and average nucleotide identity (83.6–84.6 %) values clearly indicated that strain PS13T represents a distinct species of the genus Formosa . The major fatty acids were C15 : 0 iso, C16 : 1 ω6c/C16 : 1 ω7c and C15 : 1 iso G. The genomic DNA G+C content of the strain PS13T was 32.2 mol%. On the basis of polyphasic characteristics, it is suggested that strain PS13T be assigned to the genus Formosa as the type strain of a novel species, for which the name Formosa sediminum PS13T (=KCCM 43301T=CECT 9918T) sp. nov. is proposed.

Aquariibacter albus gen. nov., sp. nov., a new member of the order Burkholderiales, isolated from a freshwater aquarium

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Yingshun Cui ◽  
Chan-Yeong Park ◽  
Song-Yeon Kim ◽  
Shu-Kuan Wong ◽  
An Suk Lim ◽  
...  
Keyword(s):  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Average Amino Acid Identity ◽  
Novel Genus And Species ◽  
Bacterium Strain ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A novel bacterium, strain SJAQ100T, was isolated from a freshwater aquarium and was characterized taxonomically and phylogenetically. Strain SJAQ100T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25–37 °C on Reasoner's 2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strain SJAQ100T clustered with members of Burkholderiales incertae sedis in the order Burkholderiales , but sequence similarities to known species were less than 96.5 %. The genomic DNA G+C content of strain SJAQ100T was 71.2 mol%. Genomic comparisons of strain SJAQ100T with species in the order Burkholderiales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤22.1, ≤78.1, and ≤68.1 % respectively). Strain SJAQ100T contained C16 : 0 and C16 : 1  ω7c/C16 : 1  ω6c as major fatty acids and Q-8 as the major quinone. The major polyamines were putrescine and cadaverine. Strain SJAQ100T contained phosphatidylethanolamine and diphosphatidylglycerol as major polar lipids. Based on the genotypic, chemotaxonomic and phenotypic results, strain SJAQ100T represents a novel genus and species, Aquariibacter albus gen. nov., sp. nov., which belongs to order Burkholderiales and the class Betaproteobacteria . The type strain is SJAQ100T (=KCTC 72203T=CGMCC 1.18869T=MCC 4385T).

scholarly journals Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations

2004 ◽  
Vol 54 (6) ◽  
pp. 2185-2190 ◽  
Author(s):  
Hiroyuki Ohta ◽  
Reiko Hattori ◽  
Yuuji Ushiba ◽  
Hisayuki Mitsui ◽  
Masao Ito ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
High Sequence Similarity ◽  
Respiratory Quinone ◽  
Meat Extract ◽  
Low Concentrations ◽  
Bacterium Strain

The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213T, was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0·1–0·4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl2 was added, the cells grew quite normally and aberrant cells were no longer found at 0·1–0·5 % (w/v) NaCl. Chemotaxonomically, strain S213T contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1 and C16 : 0 as major fatty acids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213T belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500T (98·3 %), Sphingomonas pruni IFO 15498T (98·0 %), Sphingomonas asaccharolytica IFO 15499T (97·9 %) and Sphingomonas echinoides DSM 1805T (97·8 %). The results of DNA–DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213T represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213T (=JCM 12082T=CIP 107926T).

scholarly journals Novel Geobacillus thermoleovorans KNG 112 Thermophilic Bacteria from Bandaru Hot Spring: A Potential Producer of Thermostable enzymes.

2019 ◽  
pp. 134-141
Author(s):  
Kotresh K r ◽  
Neelagund S e ◽  
Gurumurthy D m
Keyword(s):  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Maximum Activity ◽  
Rrna Gene ◽  
Thermostable Enzymes ◽  
Geobacillus Thermoleovorans ◽  
Optimum Parameters ◽  
Novel Bacterium ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

Amylase and lipase producing novel bacterium (strain IC5) were isolated from Bandaru hot spring, Karnataka, India. The cell was found to be thermophilic, gram-positive, aerobic, non-motile, capable of growing at different optimum parameters of pH 7,  temperature 55°C and tolerated maximally 0-8% (w/v) NaCl, which has the ability to show good amylotic and lipolytic activities.  Phylogenetic analysis of the bacterium using the 16S rRNA gene was revealed that the strain belongs to genus Geobacillus. The isolated strain IC5 was in close resemblance with the gene of Geobacillus thermoleovorans EC-5 having 99% of similarities. During the production of amylase, the maximum activity was found when temperature and pH ranged from 50 to 60 ºC and from 7 to 8 respectively. The strain used starch as a carbon source with an agitation speed of 120rpm for maximal amylase production.

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