scholarly journals Isachenkonia alkalipeptolytica gen. nov. sp. nov., a new anaerobic, alkaliphilic proteolytic bacterium capable of reducing Fe(III) and sulfur

2020 ◽  
Vol 70 (8) ◽  
pp. 4730-4738 ◽  
Author(s):  
Daria G. Zavarzina ◽  
Tatyana N. Zhilina ◽  
Nadegda A. Kostrikina ◽  
Stepan V. Toshchakov ◽  
Ilya V. Kublanov
Keyword(s):  
Soda Lake ◽  
Sodium Caseinate ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
The Novel ◽  
Protein Marker ◽  
Content Type ◽  
Link Type ◽  
Novel Genus And Species ◽  
Proteolytic Bacterium

An obligately alkaliphilic, anaerobic, proteolytic bacterium was isolated from a sample of Tanatar III soda lake sediment (Altai region, Russia) and designated as strain Z-1701T. Cells of strain Z-1701T were short, straight, motile Gram-stain-positive rods. Growth of Z-1701T obligately depended on the presence of sodium carbonate. Strain Z-1701T could utilize various peptides mixtures, such as beef and yeast extracts, peptone, soytone, trypticase and tryptone, as well as such proteins as albumin, gelatin and sodium caseinate. It was able to grow oligotrophically with 0.02 g l−1 yeast extract as the sole energy and carbon source. Carbohydrates did not support the growth of strain Z-1701T. The main products released during the growth of strain Z-1701T on tryptone were formate, acetate and ammonium. Strain Z-1701T was able to reduce ferrihydrite, Fe(III)-EDTA, anthraquinone-2,6-disulfonate and elemental sulfur, using proteinaceous substrates as electron donors. In all cases the presence of the electron acceptor in the medium stimulated growth. The main cellular fatty acids were iso-C15 : 0, iso-C15 : 0 aldehyde, iso-C15 : 1 ω6, C16 : 0, iso-C17 : 0 aldehyde, C16 : 0 aldehyde and C14 : 0. The DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on the concatenated alignment of 120 protein-marker sequences revealed that strain Z-1701T falls into a cluster with the genus Tindallia , family Clostridiaceae . 16S rRNA gene sequence identity between strain Z-1701T and Tindallia species were 88.3–89.75 %. On the basis of its phenotypic characteristics and phylogenetic position, the novel isolate is considered to be a representative of a novel genus and species for which the name Isachenkonia alkalipeptolytica gen. nov., sp. nov. is proposed, with Z-1701T (=JCM 32929Т=DSM 109060Т=VKM B-3261Т) as its type strain.

Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4456-4461 ◽  
Author(s):  
Daria G. Zavarzina ◽  
Tatyana N. Zhilina ◽  
Boris B. Kuznetsov ◽  
Tatyana V. Kolganova ◽  
Georgy A. Osipov ◽  
...  
Keyword(s):  
Yeast Extract ◽  
Sequence Similarity ◽  
Soda Lake ◽  
Rrna Gene ◽  
Donor Strain ◽  
Content Type ◽  
Link Type ◽  
Nacl Concentration ◽  
Novel Genus And Species ◽  
Ph Range

An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001T. Cells of strain Z-1001T were straight, Gram-positive rods, slowly motile. Strain Z-1001T was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25–9.5 (at 40 °C), a temperature range from 20 to 57 °C with an optimum at 45–50 °C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2–1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001T. Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001T reduced S 2 O 3 2 − , NO 3 − , AsO 4 3 − , Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l−1. The main fatty acids were C16 : 0, C16 : 1ω7c , C18 : 0 and C18 : 1ω9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001T is a member of family Natranaerobiaceae , clustering with the type strain of Natranaerobius thermophilus (95.8–96.0 % sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001T ( = DSM 24923T = VKM B-2666T) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov.

scholarly journals Canibacter oris gen. nov., sp. nov., isolated from an infected human wound

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1635-1640 ◽  
Author(s):  
M. Aravena-Román ◽  
T. J. J. Inglis ◽  
C. Siering ◽  
P. Schumann ◽  
A. F. Yassin
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Novel Genus And Species ◽  
Chemical Studies ◽  
A Cell

A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria , displaying 91.6 % to 96 % sequence similarity with members of the family Microbacteriaceae . Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter . Chemical studies revealed the presence of a cell-wall murein based on l-lysine (type B1α), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T ( = DSM 27064T = CCUG 64069T).

Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 254-259 ◽  
Author(s):  
Amit Kumar Singh ◽  
Nidhi Garg ◽  
Pushp Lata ◽  
Roshan Kumar ◽  
Vivek Negi ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Species Cluster ◽  
Physiological Tests

An orange-pigmented bacterial strain, designated LP100T, was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100T occupied a distinct phylogenetic position in the Pontibacter species cluster, showing highest similarity with Pontibacter lucknowensis DM9T (97.4 %). Levels of similarity to strains of other Pontibacter species ranged between 94.0 and 96.8 %. Strain LP100T contained MK-7 as the predominant menaquinone and sym-homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain LP100T were anteiso-C17 : 0 A, iso-C15 : 0 and iso-C18 : 1 H. The polar lipid profile of strain LP100T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100T was 58.2 mol%. The results of DNA–DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus Pontibacter . Therefore, strain LP100T represents a novel species of the genus Pontibacter for which the name Pontibacter indicus is proposed. The type strain is LP100T ( = CCM8435T = MCC2027T).

Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L.

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1241-1248 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Chuan Jiong Hu ◽  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Jatropha Curcas ◽  
Sequence Similarity ◽  
Distance Matrix ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Endophytic Actinobacterium

A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650T forms an individual line of descent and is related to certain members of the suborder Frankineae , order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae ) and Acidothermus (family Acidothermaceae ) and the other by members of the genera Geodermatophilus , Blastococcus and Modestobacter (family Geodermatophilaceae ). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C18 : 1ω9c, anteiso-C17 : 0 and C17 : 1ω8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650T represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650T ( = DSM 45627T = KACC 16232T).

Asinibacterium lactis gen. nov., sp. nov., a member of the family Chitinophagaceae , isolated from donkey (Equus asinus) milk

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3180-3185 ◽  
Author(s):  
Dong-Geol Lee ◽  
Ji-Min Park ◽  
Heecheol Kang ◽  
So-Young Hong ◽  
Kyung Real Lee ◽  
...  
Keyword(s):  
Milk Powder ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type ◽  
Equus Asinus ◽  
The Family ◽  
Novel Genus And Species

A novel bacterial strain, designated LCJ02T, was isolated on R2A agar from donkey (Equus asinus) milk powder and subjected to a taxonomic study using a polyphasic approach. Strain LCJ02T showed a Gram-negative reaction, was non-motile, non-spore-forming and possessed rod-shaped cells and yellow-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate formed a cluster with several uncultured bacterial clones and with cultured members of the genera Hydrotalea , Sediminibacterium and Lacibacter (family Chitinophagaceae , phylum Bacteroidetes ). The gene sequence similarities with respect to the type strains of recognized species from the above genera and other phylogenetic neighbours ranged from 89.3 to 92.9 %. The G+C content of the genomic DNA was 49.2 mol%, the only isoprenoid quinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipids of strain LCJ02T were phosphatidylethanolamine, two unidentified aminophospholipids, one unidentified aminolipid and five unidentified lipids. The results of physiological and biochemical tests allowed phenotypic differentiation of strain LCJ02T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate LCJ02T represents a novel genus and species in the family Chitinophagaceae for which the name Asinibacterium lactis gen. nov., sp. nov. is proposed. The type strain is LCJ02T ( = KCCM 90108T = JCM 18484T).

Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 551-558 ◽  
Author(s):  
Dan Wang ◽  
Hongliang Liu ◽  
Shixue Zheng ◽  
Gejiao Wang
Keyword(s):  
Type Species ◽  
Rhodobacter Capsulatus ◽  
Photosynthetic Bacterium ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Novel Genus And Species ◽  
Major Respiratory Quinone

A Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped, non-photosynthetic bacterial strain, DW2-9T, was isolated from soil. The highest 16S rRNA gene sequence similarities were found to Rhodobacter capsulatus ATCC 11166T (97.1 %), Rhodobacter viridis JA737T (96.4 %), Rhodobacter maris JA276T (96.2 %), Rhodobacter veldkampii ATCC 35703T (96.0 %), Haematobacter massiliensis CCUG 47968T (96.0 %), Haematobacter missouriensis CCUG 52307T (95.9 %) and Rhodobacter aestuarii JA296T (95.7 %). The genomic DNA G+C content was 67.2 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>5 %) were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c and summed feature 3 (one or more of iso-C15 : 0 2-OH, C16 : 1ω6c and C16 : 1ω7c). However, unlike species of the genus Rhodobacter , strain DW2-9T neither formed internal photosynthetic membranes nor produced photosynthetic pigments. DNA–DNA hybridization between strain DW2-9T and R. capsulatus JCM 21090T showed a relatedness of 33 %. Strain DW2-9T contained phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid as major polar lipids, which differed from those of species of the genera Rhodobacter and Haematobacter . In addition to the differences in phylogenetic position and polar lipid types, strain DW2-9T could be distinguished from species of the genus Haematobacter by the cultivation conditions. On the basis of our polyphasic taxonomic analysis, strain DW2-9T is considered to represent a novel genus and species, for which the name Paenirhodobacter enshiensis gen. nov., sp. nov. is proposed. The type strain of Paenirhodobacter enshiensis is DW2-9T ( = CCTCC AB 2011145T = KCTC 15169T). Emended descriptions of the genera Rhodobacter and Haematobacter are also proposed.

scholarly journals Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov.

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3353-3359 ◽  
Author(s):  
Ryosuke Nakai ◽  
Miyuki Nishijima ◽  
Nozomi Tazato ◽  
Yutaka Handa ◽  
Fatma Karray ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
The Novel ◽  
Filamentous Bacterium ◽  
Gram Negative ◽  
Content Type ◽  
Link Type ◽  
Novel Genus And Species

A phylogenetically novel proteobacterium, strain Shr3T, was isolated from sand gravels collected from the eastern margin of the Sahara Desert. The isolation strategy targeted bacteria filterable through 0.2-µm-pore-size filters. Strain Shr3T was determined to be a Gram-negative, aerobic, non-motile, filamentous bacterium. Oxidase and catalase reactions were positive. Strain Shr3T showed growth on R2A medium, but poor or no growth on nutrient agar, trypticase soy agar and standard method agar. The major isoprenoid quinone was menaquinone-7. The dominant cellular fatty acids detected were C16 : 1ω5c and C16 : 0, and the primary hydroxy acid present was C12 : 0 3-OH. The DNA G+C content was 54.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Shr3T was affiliated with an uncultivated lineage of the phylum Proteobacteria ; the nearest known type strain, with 83 % sequence similarity, was Desulfomicrobium orale DSM 12838T in the class Deltaproteobacteria . The isolate and closely related environmental clones formed a novel class-level clade in the phylum Proteobacteria with high bootstrap support (96–99 %). Based on these results, the novel class Oligoflexia classis nov. in the phylum Proteobacteria and the novel genus and species Oligoflexus tunisiensis gen. nov., sp. nov. are proposed for strain Shr3T, the first cultivated representative of the Oligoflexia. The type strain of Oligoflexus tunisiensis is Shr3T ( = JCM 16864T = NCIMB 14846T). We also propose the subordinate taxa Oligoflexales ord. nov. and Oligoflexaceae fam. nov. in the class Oligoflexia.

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

scholarly journals Halostagnicola bangensis sp. nov., an alkaliphilic haloarchaeon from a soda lake

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 754-759 ◽  
Author(s):  
Paulina Corral ◽  
Angela Corcelli ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Soda Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

An extremely haloalkaphilic archaeon, strain T26T, belonging to the genus Halostagnicola , was isolated from sediment of the soda lake Bange in the region of Tibet, China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain T26T was closely related to Halostagnicola alkaliphila 167-74T (98.4 %), Halostagnicola larsenii XH-48T (97.5 %) and Halostagnicola kamekurae 194-10T (96.8 %). Strain T26T grew optimally in media containing 25 % (w/v) salts, at pH 9.0 and 37 °C in aerobic conditions. Mg2+ was not required for growth. The cells were motile, pleomorphic and Gram-stain-variable. Colonies of this strain were pink pigmented. Hypotonic treatment caused cell lysis. The polar lipids of the isolate consisted of C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phospholipids components. Glycolipids were not detected, in contrast to the two neutrophilic species of this genus. The genomic DNA G+C content of strain T26T was 60.1 mol% and DNA–DNA hybridization showed a relatedness of 19 and 17 % with Halostagnicola alkaliphila CECT 7631T and Halostagnicola larsenii CECT 7116T, respectively. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA–DNA hybridization studies revealed that strain T26T belongs to the genus Halostagnicola , and represents a novel species for which the name Halostagnicola bangensis sp. nov. is proposed. The type strain is T26T ( = CECT 8219T = IBRC-M 10759T = JCM 18750T).

Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1625-1629 ◽  
Author(s):  
Guillaume Borrel ◽  
Keith Joblin ◽  
Annie Guedon ◽  
Jonathan Colombet ◽  
Vincent Tardy ◽  
...  
Keyword(s):  
Rumen Fluid ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Meromictic Lake ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Lake Pavin

An autotrophic, hydrogenotrophic methanogen, designated strain 17A1T, was isolated from the profundal sediment of the meromictic Lake Pavin, France. The cells of the novel strain, which were non-motile, Gram-staining-negative rods that measured 2–15 µm in length and 0.2–0.4 µm in width, grew as filaments. Strain 17A1T grew in a mineral medium and its growth was stimulated by the addition of yeast extract, vitamins, acetate or rumen fluid. Penicillin, vancomycin and kanamycin reduced growth but did not completely inhibit it. Growth occurred at 14–41 °C (optimum 30 °C), at pH 5.0–8.5 (optimum pH 6.5) and with 0–0.4 M NaCl (optimum 0.1 M). The novel strain utilized H2/CO2 and methanol/H2 as substrates but not formate, acetate, methylamine/H2, isobutanol or 2-propanol. Its genomic DNA G+C content was 37.0 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain 17A1T appeared to be a member of the genus Methanobacterium , with Methanobacterium beijingense 8-2T (96.3 % sequence similarity) identified as the most closely related established species. Based on phenotypic and phylogenetic data, strain 17A1T represents a novel species of methanogen within the genus Methanobacterium , for which the name Methanobacterium lacus sp. nov. is proposed. The type strain is 17A1T ( = DSM 24406T = JCM 17760T).

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