Comparing Two Common DNA Extraction Kits for the Characterization of Symbiotic Microbial Communities from Ascidian Tissue.

abstract：:Over the past few decades, degradative plasmids have been isolated from bacteria capable of degrading a variety of both natural and man-made compounds. Degradative plasmids belonging to three incompatibility (Inc) groups in Pseudomonas (IncP-1, P-7, and P-9) have been well studied in terms of their replication, mainte...

journal_title：Microbes and environments

authors： Shintani M,Takahashi Y,Yamane H,Nojiri H

更新日期：2010-01-01 00:00:00

abstract：:To clarify altitudinal changes in the bacterial community on Gulkana Glacier in Alaska, we analyzed bacterial 16S rRNA gene by low-cycle PCR amplification, denaturing gradient gel electrophoresis (DGGE), and culturing in a snowmelt medium at 4°C. Low-cycle PCR-based cloning revealed the presence of 100 bacterial OTUs;...

journal_title：Microbes and environments

authors： Segawa T,Takeuchi N,Ushida K,Kanda H,Kohshima S

更新日期：2010-01-01 00:00:00

abstract：:Marine fungus-like eukaryotic unicellular protists (thraustochytrids) are considered to play an important role in the marine microbial food web. However, their abundance, distribution, and relative biomass in coastal waters have not yet been examined in detail. By using a flow cytometry method (FCM) for the rapid enum...

journal_title：Microbes and environments

authors： Duan Y,Sen B,Xie N,Paterson JS,Chen Z,Wang G

更新日期：2018-07-04 00:00:00

abstract：:Fusarium oxysporum is an ascomycetous fungus that is well-known as a soilborne plant pathogen. In addition, a large population of nonpathogenic F. oxysporum (NPF) inhabits various environmental niches, including the phytosphere. To obtain an insight into the origin of plant pathogenic F. oxysporum, we focused on the t...

journal_title：Microbes and environments

authors： Inami K,Kashiwa T,Kawabe M,Onokubo-Okabe A,Ishikawa N,Pérez ER,Hozumi T,Caballero LA,de Baldarrago FC,Roco MJ,Madadi KA,Peever TL,Teraoka T,Kodama M,Arie T

更新日期：2014-01-01 00:00:00

abstract：:A newly-developed molecular method, hierarchical oligonucleotide primer extension (HOPE), was used to analyze various groups within the species Cylindrospermopsis raciborskii. PCR-amplified internally transcribed spacer sequences of 16S-23S from C. raciborskii in reservoir samples of Taiwan and Kinmen were examined. O...

journal_title：Microbes and environments

authors： Wu JH,Hsu MH,Hung CH,Tseng IC,Lin TF

更新日期：2010-01-01 00:00:00

abstract：:The aim of the present study was to investigate the prokaryotic community structure of the anaerobic ciliate, Metopus sp. using rRNA sequencing, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM). Metopus sp. was physically separated from anaerobic granular sludge in a domestic waste...

journal_title：Microbes and environments

authors： Hirakata Y,Oshiki M,Kuroda K,Hatamoto M,Kubota K,Yamaguchi T,Harada H,Araki N

更新日期：2015-01-01 00:00:00

abstract：:A comprehensive survey of bacterial and archaeal community structures within granular sludges taken from twelve different types of full-scale, food-processing wastewater-treating, upflow anaerobic sludge blanket (UASB) reactors was performed with a 16S rRNA gene-based clone library method. In total, 1,282 bacterial 16...

journal_title：Microbes and environments

authors： Narihiro T,Terada T,Kikuchi K,Iguchi A,Ikeda M,Yamauchi T,Shiraishi K,Kamagata Y,Nakamura K,Sekiguchi Y

更新日期：2009-01-01 00:00:00

abstract：:Arsenic (As) is a widely distributed toxic element in the environment and microorganisms have developed resistance mechanisms in order to tolerate it. The cellular response of the chemoorganotrophic arsenite (As[III])-oxidizing α-Proteobacteria, Sinorhizobium sp. strain A2, to arsenic was examined in the present study...

journal_title：Microbes and environments

authors： Fukushima K,Huang H,Hamamura N

更新日期：2015-01-01 00:00:00

abstract：:A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. In...

journal_title：Microbes and environments

authors： Kongpol A,Kato J,Tajima T,Vangnai AS

更新日期：2012-01-01 00:00:00

abstract：:The emergence of drug-resistant bacteria is a severe problem in aquaculture. The ability of drug resistance genes to transfer from a bacterial cell to another is thought to be responsible for the wide dissemination of these genes in the aquaculture environment; however, little is known about the gene transfer mechanis...

journal_title：Microbes and environments

authors： Nonaka L,Maruyama F,Miyamoto M,Miyakoshi M,Kurokawa K,Masuda M

更新日期：2012-01-01 00:00:00

abstract：:Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid...

journal_title：Microbes and environments

authors： Tang X,Xie G,Shao K,Dai J,Chen Y,Xu Q,Gao G

更新日期：2015-01-01 00:00:00

abstract：:Soil and rhizosphere environments were examined in order to determine the identity and relative abundance of bacteria that catabolize d- and l-amino acids as the sole source of carbon and nitrogen. All substrates were readily catabolized by bacteria from both environments, with most d-amino acids giving similar CFU co...

journal_title：Microbes and environments

authors： Radkov AD,McNeill K,Uda K,Moe LA

更新日期：2016-06-25 00:00:00

abstract：:Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 1509...

journal_title：Microbes and environments

authors： Inoue J,Oshima K,Suda W,Sakamoto M,Iino T,Noda S,Hongoh Y,Hattori M,Ohkuma M

更新日期：2015-01-01 00:00:00

abstract：:We investigated the effects of the water status (flooded or non-flooded) and presence of the nosZ gene in bradyrhizobia on the bradyrhizobial community structure in a factorial experiment that examined three temperature levels (20°C, 25°C, and 30°C) and two soil types (andosol and gray lowland soil) using microcosm in...

journal_title：Microbes and environments

authors： Saeki Y,Nakamura M,Mason MLT,Yano T,Shiro S,Sameshima-Saito R,Itakura M,Minamisawa K,Yamamoto A

更新日期：2017-06-24 00:00:00

abstract：:The simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is a major limitation in investigating the community structures of bacteria associated with plants because organelle SSU rRNA genes are easily amplified by PCR using primer sets that are specific to bacteria....

journal_title：Microbes and environments

authors： Ikenaga M,Sakai M

更新日期：2014-09-17 00:00:00

abstract：:Atrazine is a triazine herbicide that is widely used to control broadleaf weeds. Its widespread use over the last 50 years has led to the potential contamination of soils, groundwater, rivers, and lakes. Its main route of complete degradation is via biological means, which is carried out by soil microbiota using a 6-s...

journal_title：Microbes and environments

authors： Fernandes AFT,Wang P,Staley C,Aparecida Silva Moretto J,Miguel Altarugio L,Chagas Campanharo S,Guedes Stehling E,Jay Sadowsky M

更新日期：2020-01-01 00:00:00

abstract：:In order to understand the relationships between understory bamboo and soil properties, we compared microbial community structures in the soil of a Betula ermanii boreal forest with Sasa kurilensis present and removed using high-throughput DNA sequencing. The presence of understory S. kurilensis strongly affected soil...

journal_title：Microbes and environments

authors： Kong B,Chen L,Kasahara Y,Sumida A,Ono K,Wild J,Nagatake A,Hatano R,Hara T

更新日期：2017-06-24 00:00:00

abstract：:Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal gut communities have been extensively studied. However, limited information is available on viruses in the termite gut. We herein report the complete genome sequence (99,517 bp) of a phage obtained during a genome analysis of "...

journal_title：Microbes and environments

authors： Pramono AK,Kuwahara H,Itoh T,Toyoda A,Yamada A,Hongoh Y

更新日期：2017-06-24 00:00:00

abstract：:Due to their obligate symbiotic nature and lack of long-term storage methods, the strain collection of arbuscular mycorrhizal (AM) fungi requires periodic proliferation using a pot culture with host plants. Therefore, a method to evaluate the purity of proliferated AM fungal cultures is critical for the quality contro...

journal_title：Microbes and environments

authors： Ohtomo R,Oka N,Morimoto S

更新日期：2019-12-27 00:00:00

abstract：:The role of microbes in the early development of ecosystems on new volcanic materials seems to be crucial to primary plant succession but is not well characterized. Here we analyzed the bacterial community colonizing 22-year-old volcanic deposits of the Miyake-jima Island (Japan) using culture-based and 16S rRNA gene ...

journal_title：Microbes and environments

authors： Lu H,Fujimura R,Sato Y,Nanba K,Kamijo T,Ohta H

更新日期：2008-01-01 00:00:00

abstract：:Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70-86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation...

journal_title：Microbes and environments

authors： Nishihara A,Thiel V,Matsuura K,McGlynn SE,Haruta S

更新日期：2018-12-28 00:00:00

abstract：:Recent studies demonstrated that phylogenetically more diverse and abundant bacteria and fungi than previously considered are responsible for denitrification in terrestrial environments. We herein examined the effects of land-use types on the community composition of those denitrifying microbes based on their nitrite ...

journal_title：Microbes and environments

authors： Fujimura R,Azegami Y,Wei W,Kakuta H,Shiratori Y,Ohte N,Senoo K,Otsuka S,Isobe K

更新日期：2020-01-01 00:00:00

abstract：:Branched nonylphenol (BNP), a degradation product of nonylphenol polyethoxylates, exerts estrogenic effects on various organisms. The genes underlying BNP degradation by Sphingobium amiense DSM 16289T were analyzed by complete genome sequencing and compared with those of the versatile BNP-degrading Sphingobium cloacae...

journal_title：Microbes and environments

authors： Ootsuka M,Nishizawa T,Hasegawa M,Kurusu Y,Ohta H

更新日期：2018-12-28 00:00:00

abstract：:Small cyanobacteria (<2 µm, pico-cyanobacteria) are abundant in waters deeper than the oxic-anoxic zone in the halocline of a saline meromictic lake, Lake Suigetsu, Fukui, Japan. We have isolated 101 strains that were grouped into six groups by means of the phycobiliprotein composition and sequence homology of the int...

journal_title：Microbes and environments

authors： Ohki K,Yamada K,Kamiya M,Yoshikawa S

更新日期：2012-01-01 00:00:00

abstract：:HcRNAV is a small icosahedral virus that infects the shellfish-killing marine dinoflagellate Heterocapsa circularisquama, which harbors a dicistronic linear single-stranded RNA (ssRNA) genome ca. 4.4 kb in length. Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, pos...

journal_title：Microbes and environments

authors： Wada K,Kimura K,Hasegawa A,Fukuyama K,Nagasaki K

更新日期：2012-01-01 00:00:00

abstract：:Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-a...

journal_title：Microbes and environments

authors： Liu D,Tago K,Hayatsu M,Tokida T,Sakai H,Nakamura H,Usui Y,Hasegawa T,Asakawa S

更新日期：2016-09-29 00:00:00

abstract：:The nifV gene encodes homocitrate synthase, the enzyme that catalyzes the formation of homocitrate, which is essential for arranging the FeMo-cofactor in the catalytic center of nitrogenase. Some host plants, such as Lotus japonicus, supply homocitrate to their symbionts, in this case, Mesorhizobium loti, which lacks ...

journal_title：Microbes and environments

authors： Hashimoto S,Wongdee J,Songwattana P,Greetatorn T,Goto K,Tittabutr P,Boonkerd N,Teaumroong N,Uchiumi T

更新日期：2019-12-27 00:00:00

abstract：:Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still con...

journal_title：Microbes and environments

authors： Urashima Y,Sonoda T,Fujita Y,Uragami A

更新日期：2012-01-01 00:00:00

abstract：:Diarrhea is often associated with marked alterations in the intestinal microbiota, termed dysbiosis; however, limited information is currently available on the intestinal microbiota in captive golden snub-nosed monkeys (Rhinopithecus roxellana) with diarrhea. We herein characterized the fecal microbiota in diarrhea an...

journal_title：Microbes and environments

authors： Zhu H,Zeng D,Wang Q,Wang N,Zeng B,Niu L,Ni X

更新日期：2018-09-29 00:00:00

abstract：:The splicing of a bacterial group II subclass B intron B.me.I1 from Bacillus megaterium chromosomes was investigated. RT-PCR and nucleic acid hybridization methods were used to understand the role of the intron-encoded protein (IEP) in the splicing of B.me.I1. An in vivo assay showed that the splicing occurred in the ...

journal_title：Microbes and environments

authors： Chien MF,Tosa S,Huang CC,Endo G

更新日期：2009-01-01 00:00:00