scholarly journals Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

2014 ◽  
Vol 29 (1) ◽  
pp. 74-81 ◽  
Author(s):  
Jun Murase ◽  
Yuriko Takenouchi ◽  
Kazufumi Iwasaki ◽  
Makoto Kimura
Keyword(s):  
Rice Field ◽  
Rrna Gene ◽  
Field Soil ◽  
Rice Field Soil

scholarly journals Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand

2006 ◽  
Vol 56 (6) ◽  
pp. 1257-1261 ◽  
Author(s):  
Liming Wang ◽  
Ying Huang ◽  
Zhiheng Liu ◽  
Michael Goodfellow ◽  
Carlos Rodríguez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rice Field ◽  
Gene Tree ◽  
Morphological Properties ◽  
Rrna Gene ◽  
New Taxon ◽  
Field Soil ◽  
Rice Field Soil

The taxonomic position of ten acidophilic actinomycetes isolated from an acidic rice-field soil was established using a polyphasic approach. 16S rRNA gene sequences determined for the isolates were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. The isolates had identical sequences and formed a distinct branch at the periphery of the Streptacidiphilus 16S rRNA gene tree. The chemotaxonomic and morphological properties of representative isolates were consistent with their assignment to the genus Streptacidiphilus. The isolates shared nearly identical phenotypic profiles that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the isolates form a homogeneous group that corresponds to a novel species in the genus Streptacidiphilus. The name proposed for this new taxon is Streptacidiphilus oryzae sp. nov.; the type strain is strain TH49T (=CGMCC 4.2012T=JCM 13271T).

scholarly journals Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1389-1395 ◽  
Author(s):  
Sanae Sakai ◽  
Masayuki Ehara ◽  
I-Cheng Tseng ◽  
Takashi Yamaguchi ◽  
Suzanna L. Bräuer ◽  
...  
Keyword(s):  
Type Species ◽  
Rice Field ◽  
Rrna Gene ◽  
Field Soil ◽  
Phenotypic Properties ◽  
Content Type ◽  
Hydrogenotrophic Methanogen ◽  
Link Type ◽  
Rice Field Soil ◽  
The 16S Rrna Gene

A novel mesophilic, hydrogenotrophic methanogen, designated strain TNRT, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNRT grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l−1 (optimally at 0 g NaCl l−1). The strain utilized H2/CO2 and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNRT was related most closely to Methanolinea tarda NOBI-1T; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNRT and M. tarda NOBI-1T represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNRT is considered to represent a novel species of the genus Methanolinea , for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNRT ( = NBRC 105659T = DSM 23604T). In addition, we also suggest family status for the E1/E2 group within the order Methanomicrobiales , for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.

Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2442-2449 ◽  
Author(s):  
Prabla Kumari ◽  
Saumya Bandyopadhyay ◽  
Subrata K. Das
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Rice Field ◽  
Rrna Gene ◽  
Field Soil ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Rice Field Soil

A novel aerobic soil actinobacterium (strain MB10T) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0–11.0 and at 16–37 °C; optimum growth was observed at 28 °C and pH 7.0–9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10T were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10T clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145T. However, DNA–DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145T, the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA reassociation studies, it is proposed that strain MB10T represents a novel species of the genus Microbacterium , for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10T ( = JCM 16837T = DSM 23396 T ).

scholarly journals Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil

2011 ◽  
Vol 61 (6) ◽  
pp. 1246-1252 ◽  
Author(s):  
Koji Kitamura ◽  
Takashi Fujita ◽  
Shinji Akada ◽  
Akio Tonouchi
Keyword(s):  
Carbon Dioxide ◽  
Rice Field ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Field Soil ◽  
Bacteria Growth ◽  
Gram Positive Bacteria ◽  
Rice Field Soil

A pure culture of an obligately anaerobic, hydrogenotrophic, methanogenic archaeon, designated strain 169T, which grows with hydrogen and carbon dioxide as the sole energy and carbon sources, was isolated from an anaerobic propionate-oxidizing enrichment culture originally obtained as an inoculant from rice-field soil in Japan. Cells of strain 169T were non-motile, Gram-reaction-variable and rod-shaped or slightly curved rods with rounded ends (1.6–5.0×0.35–0.5 µm). Strain 169T had fimbriae at both ends of the cell (up to ~10 per cell) but did not possess flagella. Ultrathin sections showed a single-layered, electron-dense cell wall about 6 nm thick, which is typical of Gram-positive bacteria. Growth was observed at 15 °C–45 °C (optimum 40 °C), at pH  6.5–9.6 (optimum pH 7.5–8.5) and in 0–70 g NaCl l−1 (0–1.2 M) (optimum 5 g NaCl l−1; 0.086 M). Strain 169T utilized only hydrogen and carbon dioxide as energy and carbon sources. The DNA G+C content was 39.3 mol%. The results of 16S rRNA gene sequence analysis indicated that strain 169T was most closely related to Methanobacterium subterraneum DSM 11074T (96.8 % sequence similarity) and Methanobacterium formicicum DSM 1535T (96.4 %). On the basis of its morphological, physiological and phylogenetic characteristics, strain 169T ( = DSM 22026T = JCM 15797T) represents a novel species of the genus Methanobacterium, for which the name Methanobacterium kanagiense sp. nov. is proposed.

scholarly journals Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil

2020 ◽  
Vol 70 (4) ◽  
pp. 2713-2718 ◽  
Author(s):  
Haoxin Lv ◽  
Nurettin Sahin ◽  
Akio Tani
Keyword(s):  
Rice Field ◽  
Draft Genome ◽  
Rrna Gene ◽  
Methylotrophic Bacteria ◽  
Field Soil ◽  
Methylamine Dehydrogenase ◽  
Content Type ◽  
Link Type ◽  
Rice Field Soil ◽  
Ph Range

A new lanthanide (Ln3+)-dependent methanol-utilizing bacterial strain, La3113T, was isolated from rice field soil and its taxonomic position was investigated using polyphasic approaches. The strain was aerobic, Gram-stain-negative, strongly motile, catalase-positive and cytochrome oxidase-positive. It could neither catalyse the hydrolysis of urea nor reduce nitrate to nitrite. Growth was observed within a temperature range of 10–40 °C and a pH range of 6–8, with optimum growth at 28 °C and pH 7. Methylamine was utilized as the single source of energy, carbon and nitrogen, and it was oxidized by methylamine dehydrogenase. C16 : 1  ω7c, C16 : 1  ω6c and C16 : 0 were the dominant cellular fatty acids. Its draft genome (2.67 Mbp and 44.9 mol% G+C content) encodes genes including three Ln3+-dependent methanol dehydrogenase (XoxF-type MDH) genes, those for formaldehyde assimilation (ribulose monophosphate pathway), formate dehydrogenases and methylamine dehydrogenases, but not Ca2+-dependent MDH (MxaFI-MDH), which characterizes the species as a Ln3+-dependent methylotroph. The 16S rRNA gene sequence showed that strain La3113T belongs to the genus Methylotenera and is closely related to Methylotenera mobilis JLW8T (98.29 % identity). The digital DNA–DNA hybridization (dDDH) values (less than 30 %) and average nucleotide identity (ANI) values (less than 85 %) between genomes of strain La3113T and related type strains were lower than the thresholds for species delineation (70 % for dDDH and 95–96 % for ANI). On the basis of these polyphasic approaches, we propose a novel Methylotenera species, Methylotenera oryzisoli sp. nov. (type strain La3113T=NBRC 111954T=DSM 103219T).

scholarly journals Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil

2010 ◽  
Vol 60 (12) ◽  
pp. 2918-2923 ◽  
Author(s):  
Sanae Sakai ◽  
Ralf Conrad ◽  
Werner Liesack ◽  
Hiroyuki Imachi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Field ◽  
Phylogenetic Analyses ◽  
Marker Gene ◽  
Rrna Gene ◽  
Specific Marker ◽  
Field Soil ◽  
Hydrogenotrophic Methanogen ◽  
Rice Field Soil

A novel hydrogenotrophic methanogen, designated strain MRE50T, was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3–2.8 μm long and 0.4–0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50T grew at 37–55 °C (optimally at 45 °C), at pH 6–7.8 (optimally at pH 7.0) and in the presence of 0–20 g NaCl l−1. The isolate utilized H2/CO2 and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker gene mcrA showed that strain MRE50T is affiliated with the order Methanocellales, previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene and mcrA gene sequences, strain MRE50T was related most closely to Methanocella paludicola SANAET. Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50T and Methanocella paludicola SANAET represent different species within the genus Methanocella. In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genus Methanocella, strain MRE50T is considered to represent a novel species of the genus Methanocella, for which the name Methanocella arvoryzae sp. nov. is proposed. The type strain is MRE50T (=NBRC 105507T =DSM 22066T).

scholarly journals Response of the protistan community of a rice field soil to different oxygen tensions

2017 ◽  
Vol 93 (5) ◽  
Author(s):  
Yuriko Takenouchi ◽  
Kazufumi Iwasaki ◽  
Jun Murase
Keyword(s):  
Rice Field ◽  
Field Soil ◽  
Rice Field Soil ◽  
Oxygen Tensions
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