Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field

2011 ◽  
Vol 61 (11) ◽  
pp. 2568-2572 ◽  
Author(s):  
Estefanía Geymonat ◽  
Lucía Ferrando ◽  
Silvana E. Tarlera
Keyword(s):  
Paddy Field ◽  
Sequence Similarity ◽  
Rice Paddy ◽  
Cellular Fatty Acid ◽  
Comparative Sequence Analysis ◽  
Rrna Gene ◽  
Type I ◽  
Methylococcus Capsulatus ◽  
Rice Paddy Field ◽  
Moderately Thermophilic

A novel methanotroph, designated strain E10T, was isolated from a rice paddy field in Uruguay. Strain E10T grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30–35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2T (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10T formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14LT, respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C16 : 0 (62.05 %). Thus, strain E10T ( = JCM 16910T  = DSM 23452T) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed.

Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1832-1837 ◽  
Author(s):  
Takuya Ogiso ◽  
Chihoko Ueno ◽  
Dayéri Dianou ◽  
Tran Van Huy ◽  
Arata Katayama ◽  
...  
Keyword(s):  
Paddy Field ◽  
Rice Paddy ◽  
Rrna Gene ◽  
Type I ◽  
Intracytoplasmic Membrane ◽  
Content Type ◽  
Rice Paddy Field ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A novel methane-oxidizing bacterium, strain Fw12E-YT, was isolated from floodwater of a rice paddy field in Japan. Cells of strain Fw12E-YT were Gram-negative, motile rods with a single polar flagellum and type I intracytoplasmic membrane arrangement. The strain grew only on methane or methanol as sole carbon and energy source. It was able to grow at 10–40 °C (optimum 30 °C), at pH 5.5–7.0 (optimum 6.5) and with 0–0.1 % (w/w) NaCl (no growth above 0.5 % NaCl). 16S rRNA gene sequence analysis showed that strain Fw12E-YT is related most closely to members of the genus Methylomonas , but at low levels of similarity (95.0–95.4 %). Phylogenetic analysis of pmoA and mxaF genes indicated that the strain belongs to the genus Methylomonas (97 and 92 % deduced amino acid sequence identities to Methylomonas methanica S1T, respectively). The DNA G+C content of strain Fw12E-YT was 57.1 mol%. Chemotaxonomic data regarding the major quinone (MQ-8) and major fatty acids (C16 : 1 and C14 : 0) also supported its affiliation to the genus Methylomonas . Based on phenotypic, genomic and phylogenetic data, strain Fw12E-YT is considered to represent a novel species of the genus Methylomonas , for which the name Methylomonas koyamae sp. nov. is proposed. The type strain is Fw12E-YT ( = JCM 16701T = NBRC 105905T = NCIMB 14606T).

scholarly journals Methylothermus subterraneus sp. nov., a moderately thermophilic methanotroph isolated from a terrestrial subsurface hot aquifer

2011 ◽  
Vol 61 (11) ◽  
pp. 2646-2653 ◽  
Author(s):  
Hisako Hirayama ◽  
Yohey Suzuki ◽  
Mariko Abe ◽  
Masayuki Miyazaki ◽  
Hiroko Makita ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Type I ◽  
Rrna Gene Sequence ◽  
Intracytoplasmic Membrane ◽  
Moderately Thermophilic

A novel methane-oxidizing bacterium, strain HTM55T, was isolated from subsurface hot aquifer water from a Japanese gold mine. Strain HTM55T was a Gram-negative, aerobic, motile, coccoid bacterium with a single polar flagellum and the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain HTM55T was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 37–65 °C (optimum 55–60 °C). The isolate grew at pH 5.2–7.5 (optimum 5.8–6.3) and with 0–1 % NaCl (optimum 0–0.3 %). The ribulose monophosphate pathway was operative for carbon assimilation. The DNA G+C content was 54.4 mol% and the major fatty acids were C16 : 0 (52.0 %) and C18 : 1ω7c (34.8 %). Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HTM55T was closely related to Methylothermus thermalis MYHTT (99.2 % 16S rRNA gene sequence similarity), which is within the class Gammaproteobacteria. However, DNA–DNA relatedness between strain HTM55T and Methylothermus thermalis MYHTT was ≤39 %. On the basis of distinct phylogenetic, chemotaxonomic and physiological characteristics, strain HTM55T represents a novel species of the genus Methylothermus, for which the name Methylothermus subterraneus sp. nov. is proposed. The type strain is HTM55T ( = JCM 13664T = DSM 19750T).

scholarly journals Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan

2005 ◽  
Vol 55 (5) ◽  
pp. 1877-1884 ◽  
Author(s):  
Jun Tsubota ◽  
Bulat Ts. Eshinimaev ◽  
Valentina N. Khmelenina ◽  
Yuri A. Trotsenko
Keyword(s):  
Sequence Analysis ◽  
Hot Spring ◽  
Methane Monooxygenase ◽  
Comparative Sequence Analysis ◽  
Rrna Gene ◽  
Type I ◽  
Particulate Methane Monooxygenase ◽  
Moderately Thermophilic ◽  
Ribulose Monophosphate Pathway ◽  
Genotypic Characteristics

A novel moderately thermophilic methanotroph, strain MYHTT, was isolated from a hot spring in Japan. The isolate grew on methane or methanol at 37–67 °C, and optimally at 57–59 °C. It was found to be a Gram-negative aerobe, with colourless colonies of non-motile coccoid cells, possessing type I intracytoplasmic membranes and regularly arranged surface layers of linear (p2) symmetry. Strain MYHTT expressed only the particulate methane monooxygenase and employed the ribulose monophosphate pathway for formaldehyde assimilation. It is a neutrophilic and halotolerant organism capable of growth at pH 6·5–7·5 (optimum pH 6·8) and in up to 3 % NaCl (optimum 0·5–1 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that strain MYHTT is most closely related to the thermophilic undescribed methanotroph ‘Methylothermus’ HB (91 % identity) and the novel halophilic methanotroph Methylohalobius crimeensis 10KiT (90 % identity). Comparative sequence analysis of particulate methane monooxygenase (pmoA) genes also confirmed the clustering of strain MYHTT with ‘Methylothermus’ HB and Methylohalobius crimeensis 10KiT (98 and 92 % derived amino acid sequence identity, respectively). The DNA G+C content was 62·5 mol%. The major cellular fatty acids were C16 : 0 (37·2 %) and C18 : 1 ω9c (35·2 %) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. On the basis of comparative phenotypic and genotypic characteristics, a new genus and species, Methylothermus thermalis gen. nov., sp. nov., is proposed, with MYHTT as the type strain (=VKM B-2345T=IPOD FERM P-19714T).

scholarly journals Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1718-1723 ◽  
Author(s):  
Yan-Ling Qiu ◽  
Xiao-zhu Kuang ◽  
Xiao-shuang Shi ◽  
Xian-zheng Yuan ◽  
Rong-bo Guo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Paddy Field ◽  
Gene Sequence ◽  
Rice Paddy ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Rice Paddy Field

A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S partobacteria’, subdivision 2 of the bacterial phylum Verrucomicrobia . Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).

scholarly journals Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake

2006 ◽  
Vol 56 (3) ◽  
pp. 563-567 ◽  
Author(s):  
Stuart P. Donachie ◽  
John P. Bowman ◽  
Maqsudul Alam
Keyword(s):  
Type Species ◽  
Proteolytic Enzymes ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Octadecenoic Acid ◽  
Comparative Sequence Analysis ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Moderately Thermophilic ◽  
Moderate Thermophile

A Gram-negative bacterium, designated LA33BT, was isolated from water collected from a hypersaline lake on uninhabited Laysan Atoll in the Northwestern Hawaiian Islands. Cells of strain LA33BT are motile, straight rods that grow between 4 and 45 °C and in media containing 1–17·5 % (w/v) NaCl. The strain oxidizes carbohydrates, nucleosides, amino acids and organic acids presented as sole carbon sources and constitutive lipolytic and proteolytic enzymes are expressed. Over 75 % of the fatty acid pool is cis-11-octadecenoic acid (18 : 1ω7c). Comparative sequence analysis of the 16S rRNA gene indicates that the strain forms a new lineage in the α-2 subclass of the Proteobacteria, with the closest recognized strains being Stappia aggregata NCIMB 2208T and Roseibium denhamense JCM 10543T, with which it shares 94–95 % sequence similarity. Strain LA33BT differs phenotypically from extant Stappia and Roseibium species, however, in that it is a moderate thermophile, it requires NaCl and tolerates higher NaCl concentrations and it does not express β-galactosidase or oxidize glycerol. On the basis of genotypic data and phenotypic characteristics, we propose that strain LA33BT does not belong to the genera Stappia or Roseibium and that it represents the type species of a new genus, Nesiotobacter. Strain LA33BT (=ATCC BAA-994T=CIP 108449T) is proposed as the type strain of the type species of this genus, with the name Nesiotobacter exalbescens gen. nov., sp. nov.

scholarly journals Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2378-2384 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Moderately Thermophilic ◽  
Facultatively Anaerobic ◽  
Novel Taxa

A novel facultatively anaerobic bacterium, strain HC45T, was isolated from sediment of a brackish meromictic lake in Japan, Lake Harutori. Cells were pleomorphic, and filamentous bodies were 5–100 μm in length. For growth, the optimum pH was 7.0 and the optimum temperature was 45–50 °C. The G+C content of the genomic DNA was 71 mol%. iso-C15 : 0 and anteiso-C15 : 0 were the major components in the cellular fatty acid profile. The predominant respiratory quinone was MK-7. Strain HC45T shared very low 16S rRNA gene sequence similarity with cultivated strains ( ≤ 85 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was distantly related to members of the family Symbiobacteriaceae and family XVII Incertae Sedis in the class Clostridia, and they formed a cluster separate from canonical species of the phylum Firmicutes. These results indicated that strain HC45T should not be placed in any existing class of the phylum Firmicutes. On the basis of phylogenetic and phenotypic characterization, Limnochorda pilosa gen. nov., sp. nov. is proposed with HC45T ( = NBRC 110152T = DSM 28787T) as the type strain, as the first representative of novel taxa, Limnochordales ord. nov., Limnochordaceae fam. nov. in Limnochordia classis. nov.

Functional soil organic matter fractions in response to long-term fertilizer management in a double-cropping paddy field of southern China

2021 ◽  
pp. 1-9
Author(s):  
Haiming Tang ◽  
Chao Li ◽  
Lihong Shi ◽  
Li Wen ◽  
Kaikai Cheng ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Paddy Field ◽  
Southern China ◽  
Rice Paddy ◽  
Chemical Fertilizer ◽  
Protection Mechanism ◽  
Rice Paddy Field ◽  
Double Cropping

Abstract Soil organic matter (SOM) and its fractions play an important role in maintaining or improving soil quality and soil fertility. Therefore, the effects of a 34-year long-term fertilizer regime on six functional SOM fractions under a double-cropping rice paddy field of southern China were studied in the current paper. The field experiment included four different fertilizer treatments: chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM) and without fertilizer input as control (CK). The results showed that coarse unprotected particulate organic matter (cPOM), biochemically, physically–biochemically and chemically protected silt-sized fractions (NH-dSilt, NH-μSilt and H-dSilt) were the main carbon (C) storage fractions under long-term fertilization conditions, accounting for 16.7–26.5, 31.1–35.6, 16.2–17.3 and 7.5–8.2% of the total soil organic carbon (SOC) content in paddy soil, respectively. Compared with control, OM treatment increased the SOC content in the cPOM, fine unprotected POM fraction, pure physically protected fraction and physico-chemically protected fractions by 58.9, 106.7, 117.6 and 28.3%, respectively. The largest proportion of SOC to total SOC in the different fractions was biochemically protected, followed by chemically and unprotected, and physically protected were the smallest. These results suggested that a physical protection mechanism plays an important role in stabilizing C of paddy soil. In summary, the results showed that higher functional SOM fractions and physical protection mechanism play an important role in SOM cycling in terms of C sequestration under the double-cropping rice paddy field.

scholarly journals Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount

2004 ◽  
Vol 54 (5) ◽  
pp. 1561-1566 ◽  
Author(s):  
Koji Mori ◽  
Takeshi Kakegawa ◽  
Yowsuke Higashi ◽  
Ko-ichi Nakamura ◽  
Akihiko Maruyama ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Growth Conditions ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Good Growth ◽  
Chain Link ◽  
Circular Structure ◽  
Hybridization Test ◽  
A Chain ◽  
Cellular Fatty Acid Profile

A novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain St55BT was isolated from a sulfide chimney in the hydrothermal field of Suiyo Seamount (Izu-Bonin Arc, Western Pacific). Cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. The isolate was a chemoheterotroph requiring yeast extract for growth. Although strain St55BT used oxygen as an electron acceptor, it could not form colonies in an oxygen concentration of more than 5 % (v/v). The isolate also used nitrate, nitrite or elemental sulfur in the absence of oxygen. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Oceanithermus profundus, belonging to the phylum ‘Deinococcus–Thermus’ (sequence similarity 99·5 %). However, strain St55BT differed from O. profundus in terms of usage of electron donors, cellular fatty acid profile and DNA G+C content. In addition, a DNA–DNA hybridization test indicated low relatedness between the isolate and O. profundus. For the reasons given above, the name Oceanithermus desulfurans sp. nov. is proposed for strain St55BT (=NBRC 100063T=DSM 15757T).

scholarly journals Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (5) ◽  
pp. 941-946 ◽  
Author(s):  
Hidenori Hayashi ◽  
Kensaku Shibata ◽  
Mitsuo Sakamoto ◽  
Shinichi Tomita ◽  
Yoshimi Benno
Keyword(s):  
Fatty Acid ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Phenotypic Characteristics ◽  
Human Faeces ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Fatty Acid Compositions

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35T were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7T and CB35T were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7T (=JCM 13464T=DSM 18205T) and CB35T (=JCM 13469T=DSM 18206T), respectively.

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