scholarly journals ‘Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov., an endosymbiotic bacterium associated with nematode species of the genus Xiphinema (Nematoda, Longidoridae)

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Juan E. Palomares-Rius ◽  
Carlos Gutiérrez-Gutiérrez ◽  
Manuel Mota ◽  
Wim Bert ◽  
Myriam Claeys ◽  
...  
Keyword(s):  
Nematode Species ◽  
Rrna Gene ◽  
Host Cell Membrane ◽  
Content Type ◽  
Transmission Electron ◽  
The Family ◽  
Curved Rods ◽  
Bacterium Strain ◽  
Partial Genome

An intracellular bacterium, strain IAST, was observed to infect several species of the plant-parasitic nematode genus Xiphinema (Xiphinema astaregiense, Xiphinema incertum, Xiphinema madeirense, Xiphinema pachtaicum, Xiphinema parapachydermum and Xiphinema vallense). The bacterium could not be recovered on axenic medium. The 16S rRNA gene sequence of IAST was found to be new, being related to the family Burkholderiaceae, class Betaproteobacteria. Fungal endosymbionts Mycoavidus cysteinexigens B1-EBT (92.9 % sequence identity) and ‘Candidatus Glomeribacter gigasporarum’ BEG34 (89.8 % identity) are the closest taxa and form a separate phylogenetic clade inside Burkholderiaceae. Other genes (atpD, lepA and recA) also separated this species from its closest relatives using a multilocus sequence analysis approach. These genes were obtained using a partial genome of this bacterium. The localization of the bacterium (via light and fluorescence in situ hybridization microscopy) is in the X. pachtaicum females clustered around the developing oocytes, primarily found embedded inside the epithelial wall cells of the ovaries, from where they are dispersed in the intestine. Transmission electron microscopy (TEM) observations supported the presence of bacteria inside the nematode body, where they occupy ovaries and occur inside the intestinal epithelium. Ultrastructural analysis of the bacterium showed cells that appear as mostly irregular, slightly curved rods with rounded ends, 0.8–1.2 µm wide and 2.5–6.0 µm long, possessing a typical Gram-negative cell wall. The peptidoglycan layer is, however, evident only occasionally and not detectable by TEM in most cells. Another irregularly occurring shell surrounding the endosymbiont cells or the cell clusters was also revealed, probably originating from the host cell membrane. Flagella or spore-like cells do not occur and the nucleoid is diffusely distributed throughout the cell. This endosymbiont is transmitted vertically through nematode generations. These results support the proposal of IAST as a new species, although its obligate intracellular and obligate endosymbiont nature prevented isolation of a definitive type strain. Strain IAST is therefore proposed as representing ‘Candidatus Xiphinematincola pachtaicus’ gen. nov., sp. nov.

scholarly journals Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2449-2454 ◽  
Author(s):  
Antonie H. van Gelder ◽  
Diana Z. Sousa ◽  
W. Irene C. Rijpstra ◽  
Jaap S. Sinninghe Damsté ◽  
Alfons J. M. Stams ◽  
...  
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Curved Rods ◽  
Bacterium Strain ◽  
Ph Range

A novel anaerobic succinate-producing bacterium, strain ZWBT, was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4–0.5 µm in diameter and 2–3 µm in length), and stained Gram-negative. The temperature range for growth was 25–40 °C, with an optimum at 37 °C. The pH range for growth was 7.0–9.0, with an optimum at pH 7.5. Strain ZWBT was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWBT. The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14 : 0 and iso-C16 : 0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWBT belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006T (92.1 %). Based on the physiological features and phylogenetic analysis, strain ZWBT represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWBT ( = DSM 27333T = JCM 19283T).

scholarly journals Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis

2018 ◽  
Vol 6 (14) ◽  
Author(s):  
Sarah Hahnke ◽  
Christian Abendroth ◽  
Thomas Langer ◽  
Francisco M. Codoñer ◽  
Patrice Ramm ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biomass Hydrolysis ◽  
Content Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain ◽  
Anaerobic Biomass

ABSTRACT A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera.

scholarly journals Agaribacter marinus gen. nov., sp. nov., an agar-degrading bacterium from surface seawater

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2416-2423 ◽  
Author(s):  
Maki Teramoto ◽  
Miyuki Nishijima
Keyword(s):  
Phylogenetic Analyses ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Surface Seawater ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
The Family ◽  
Bacterium Strain

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8T, was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Alteromonadaceae and clustered distantly with members of the genus Glaciecola (≤94.0 % similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c and the major hydroxy fatty acid was C12 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8T represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8T ( = NBRC 110023T = LMG 28167T).

scholarly journals Flavicella marina gen. nov., sp. nov., a carotenoid-producing bacterium from surface seawater

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 799-804 ◽  
Author(s):  
Maki Teramoto ◽  
Miyuki Nishijima
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Novel Genus And Species ◽  
Bacterium Strain ◽  
Kochi Prefecture ◽  
Type Strains

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped or spherical bacterium, strain 2A-7T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced a pigment(s), the absorption spectrum of which closely resembled that of β-carotene. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and clustered distantly with the type strains of species of the genus Lutibacter (up to 93.9 % similarity). The DNA G+C content was 34.1 mol%. The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-7T represents a novel genus and species, for which the name Flavicella marina gen. nov., sp. nov. is proposed. The type strain of Flavicella marina is 2A-7T ( = NBRC 110145T = KCTC 42197T).

scholarly journals Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1075-1080 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Osamu Koide ◽  
Tohru Kobayashi ◽  
Kozue Mori ◽  
Shigeru Shimamura ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
Shimokita Peninsula ◽  
The Family ◽  
Bacterium Strain ◽  
Isoprenoid Quinones ◽  
Deep Subseafloor

A novel, facultatively anaerobic bacterium (strain JAM-BA0501T) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501T were Gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501T indicated a distant relationship to strains representing genera within the order Bacteroidales , such as Alkaliflexus imshenetskii Z-7010T (91.1 % similarity), Marinilabilia salmonicolor ATCC 19041T (86.2 %) and Anaerophaga thermohalophila Fru22T (89.3 %). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501T is considered to represent a novel species of a new genus within the family Marinilabiliaceae , for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501T ( = JCM 15548T  = NCIMB 14482T).

scholarly journals Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2198-2203 ◽  
Author(s):  
A. Srinivas ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Bacterium Strain

A Gram-stain-negative, rod-shaped, phototrophic bacterium, strain JA793T, was isolated from rhizosphere soil of paddy. The strain was capable of growing phototrophically and chemotrophically. Bacteriochlorophyll-a and carotenoids of the spirilloxanthin series were present as photosynthetic pigments. The major fatty acid of strain JA793T was C18 : 1ω7c/C18 : 1ω6c (>65.7 %), with minor amounts of C16 : 0, C16 : 1ω7c/C16 : 1ω6c, C20 : 2ω6,9c, C16 : 0 3-OH, C14 : 0 and C18 : 0 also present. Ubiquinone-10 and rhodoquinone-10 were present as primary quinones. Phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were the major polar lipids, while minor amounts of amino lipids and unidentified lipids were also present. The G+C content of genomic DNA of strain JA793T was 68.7 mol%. 16S rRNA gene-based EzTaxon-e blast search analysis of strain JA793T indicated highest sequence similarity with members of the genus Rhodoplanes in the family Hyphomicrobiaceae of the class Alphaproteobacteria . Strain JA793T had high sequence similarity with Rhodoplanes elegans AS130T (98.6 %), Rhodoplanes roseus 941T (98 %), Rhodoplanes pokkaliisoli JA415T (97.5 %) and Rhodoplanes piscinae JA266T (97.3 %) and other members of the genus Rhodoplanes (<97 %). However, strain JA266T was related by <59 % (based on DNA–DNA hybridization) to Rhodoplanes elegans DSM 11907T ( = AS130T), Rhodoplanes roseus DSM 5909T ( = 941T), Rhodoplanes pokkaliisoli JA415T and Rhodoplanes piscinae JA266T. The genomic information was well supported by phenotypic and chemotaxonomic data to classify strain JA793T as a representative of a novel species in the genus Rhodoplanes , for which the name Rhodoplanes oryzae sp. nov. is proposed. The type strain is JA793T ( = NBRC 109406T = KCTC 15260T).

scholarly journals Draft Genome Sequence of Strain P7-3-5, a New Flavobacteriaceae Bacterium Isolated from Intertidal Sand

2012 ◽  
Vol 194 (23) ◽  
pp. 6632-6632
Author(s):  
Xi-Ying Zhang ◽  
Bin-Bin Xie ◽  
Qi-Long Qin ◽  
Ang Liu ◽  
Xiu-Lan Chen ◽  
...  
Keyword(s):  
Draft Genome ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Intertidal Sand ◽  
The Family ◽  
Bacterium Strain ◽  
Distinct Phylogenetic Lineage ◽  
The 16S Rrna Gene

ABSTRACTTheFlavobacteriaceaebacterium strain P7-3-5 was isolated from intertidal sand of the Yellow Sea, China. Analysis of the 16S rRNA gene sequences showed that strain P7-3-5 formed a distinct phylogenetic lineage within the familyFlavobacteriaceae.The genome of strain P7-3-5 was sequenced to facilitate the physiological, ecological, and evolutionary studies of the bacteria within the familyFlavobacteriaceae.

Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1284-1288 ◽  
Author(s):  
Liang Wang ◽  
Sang-Hoon Baek ◽  
Yingshun Cui ◽  
Hyung-Gwan Lee ◽  
Sung-Taik Lee
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Paenibacillus Alvei ◽  
The Family ◽  
Bacterium Strain

A Gram-positive, rod-shaped, xylanolytic, spore-forming bacterium, strain GTH-3T, was isolated from a tidal flat adjacent to Ganghwa Island, Republic of Korea, and was characterized to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain GTH-3T was shown to belong to the family Paenibacillaceae , being most closely related to the type strains of Paenibacillus ginsengisoli (94.9 %), Paenibacillus anaericanus (94.8 %), Paenibacillus urinalis (94.4 %), Paenibacillus cookii (94.2 %), Paenibacillus alvei (94.1 %) and Paenibacillus chibensis (94.0 %). The G+C content of the genomic DNA of strain GTH-3T was 45.9±0.2 mol% (mean±sd). The major menaquinone was MK-7. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain GTH-3T to the genus Paenibacillus . The results of physiological and biochemical tests allowed strain GTH-3T to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus . Strain GTH-3T is therefore considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus sediminis sp. nov. is proposed. The type strain is GTH-3T ( = DSM 23491T  = LMG 25635T).

Flaviflexus huanghaiensis gen. nov., sp. nov., an actinobacterium of the family Actinomycetaceae

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1863-1867 ◽  
Author(s):  
Zong-Jun Du ◽  
Ting-Ting Miao ◽  
Xue-Zheng Lin ◽  
Qian-Qian Liu ◽  
Guan-Jun Chen
Keyword(s):  
Molecular Characteristics ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Temperature Range ◽  
The Family ◽  
Unknown Phospholipid ◽  
Curved Rods ◽  
Ph Range

Strain H5T was isolated from a sediment sample collected from the coastal area of Qingdao, China. The cells were Gram-stain-positive, non-motile, straight or curved rods. The temperature range for growth was 20–37 °C and the pH for growth ranged from 6.5 to 9.0, with optimum growth occurring in the temperature range 28–30 °C and pH range 7.5–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl (optimum, 0–2 %). Strain H5T had MK-9, MK-9(H2) and MK-9(H4) as the major menaquinones and C18 : 1ω9c, C16 : 0, C14 : 0, C18 : 0 and C16 : 1ω9c as major fatty acids. The cell-wall peptidoglycan type was A5α l-Lys-l-Ala-l-Lys-d-Glu. The major polar lipids were phosphatidylglycerol (PG), an unknown phospholipid (PL1) and two unknown phosphoglycolipids (PGL1, PGL2). An unknown phospholipid (PL2) and two unknown glycolipids (GL1, GL2) were present in moderate to minor amounts in the polar lipid profile. The genomic DNA G+C content was 61.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H5T represents a novel lineage in the family Actinomycetaceae . On the basis of phenotypic, physiological and molecular characteristics, it is proposed that the novel isolate should be classified as a novel species in a new genus: Flaviflexus huanghaiensis gen. nov., sp. nov., with strain H5T ( = DSM 24315T = CICC 10486T) as the type strain of the type species.

Aquihabitans daechungensis gen. nov., sp. nov., an actinobacterium isolated from reservoir water

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2970-2974 ◽  
Author(s):  
Long Jin ◽  
Hangsak Huy ◽  
Kwang Kyu Kim ◽  
Hyung-Gwan Lee ◽  
Hee-Sik Kim ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reservoir Water ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Half Strength ◽  
Bacterium Strain ◽  
Rrna Gene Sequencing

A novel Gram-reaction-positive bacterium, strain CH22-21T, was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Cells of strain CH22-21T were non-motile, ciliated short rods that formed creamy-white colonies on half-strength modified R2A agar. Chemotaxonomic results showed menaquinone MK-9(H6) as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside as major polar lipids, 16 : 1ω5c, 16 : 0, 17 : 1ω8c and 18 : 1ω9c as major fatty acids, and a DNA G+C content of 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the order Acidimicrobiales , showing similarity values of <92.3 % with its closest phylogenetic neighbours. The combined genotypic and phenotypic data showed that strain CH22-21T could be distinguished from all genera within the order Acidimicrobiales and represented a novel species of a new genus in the family Iamiaceae , for which the name Aquihabitans dachungensis gen. nov., sp. nov. is proposed. The type strain of Aquihabitans dachungensis is CH22-21T ( = KCTC 19849T = JCM 17787T).

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