scholarly journals 16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

2019 ◽  
Vol 10 ◽  
Author(s):  
Madangchanok Imchen ◽  
Ranjith Kumavath ◽  
Aline B. M. Vaz ◽  
Aristóteles Góes-Neto ◽  
Debmalya Barh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Field ◽  
Growth Stages ◽  
Rrna Gene

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 Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1296-1303 ◽  
Author(s):  
Haruka Horino ◽  
Takashi Fujita ◽  
Akio Tonouchi
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rice Field ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type

An obligately anaerobic bacterial strain designated T-1-35T was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35T stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8–1.0×3.5–15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35T exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15–40 °C, with an optimum at 35 °C. The pH range for growth was 5.5–9.0, with an optimum at pH 8.0–8.5 (slightly alkaliphilic). Strain T-1-35T fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35T belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35T was Bacteroides cellulosolvens WM2T, with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35T was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35T is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35T ( = DSM 27016T = NBRC 109520T). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species Bacteroides cellulosolvens Murray et al. 1984 is proposed to be reclassified in the new genus Pseudobacteroides as Pseudobacteroides cellulosolvens gen. nov., comb. nov., with the type strain WM2T ( = ATCC 35603T = DSM 2933T = NRCC 2944T).

scholarly journals Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta

2005 ◽  
Vol 55 (2) ◽  
pp. 935-939 ◽  
Author(s):  
Marta M. Sánchez ◽  
Dagmar Fritze ◽  
Ana Blanco ◽  
Cathrin Spröer ◽  
Brian J. Tindall ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Field ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Paenibacillus Illinoisensis ◽  
Ebro River Delta ◽  
Paenibacillus Barcinonensis ◽  
Sequence Similarities

A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10–40 °C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C15 : 0. Comparison of 16S rRNA gene sequences showed that strain BP-23T fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97·4 %), Paenibacillus pabuli (97·1 %) and Paenibacillus amylolyticus (96·9 %). The DNA–DNA relatedness of strain BP-23T with respect to these three species was very low (32·7, 31·6 and 23·0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23T should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23T (=CECT 7022T=DSM 15478T).

scholarly journals Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition

2021 ◽  
Vol 12 ◽  
Author(s):  
Ananda Y. Bandara ◽  
Dilooshi K. Weerasooriya ◽  
Ryan V. Trexler ◽  
Terrence H. Bell ◽  
Paul D. Esker
Keyword(s):  
Network Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Microbial Interactions ◽  
Growth Stages ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Microbial Composition ◽  
Site Type

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.

Leeia oryzae gen. nov., sp. nov., isolated from a rice field in Korea

2007 ◽  
Vol 57 (6) ◽  
pp. 1204-1208 ◽  
Author(s):  
Jee-Min Lim ◽  
Che Ok Jeon ◽  
Gye Suk Lee ◽  
Dong-Jin Park ◽  
Ui-Gum Kang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rice Field ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Novel Genus And Species ◽  
Distinct Lineage

A strictly aerobic, non-spore-forming, Gram-negative bacterium, designated strain HW7T, was isolated from a rice field in Korea. Cells of strain HW7T were short rod-shaped and motile with single polar flagella. The major cellular fatty acids of strain HW7T were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 56 mol% and the major isoprenoid quinone was Q-8. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HW7T forms a distinct lineage with respect to closely related genera within the class Betaproteobacteria and that the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the physiological and phylogenetic data, strain HW7T represents a novel genus and species of the Betaproteobacteria, for which the name Leeia oryzae gen. nov., sp. nov. is proposed. The type strain is HW7T (=KCTC 12585T=DSM 17879T).

scholarly journals Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1803-1809 ◽  
Author(s):  
Atsuko Ueki ◽  
Hiroshi Akasaka ◽  
Atsuya Satoh ◽  
Daisuke Suzuki ◽  
Katsuji Ueki
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rice Field ◽  
Plant Residue ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Irrigated Rice ◽  
Rice Field Soil

Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

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).

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

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