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Microbes and Environments

Takahiro Ogawa, Shohei Hattori, Kazuki Kamezaki, Hiromi Kato, Naohiro Yoshida, Yoko Katayama
Carbonyl sulfide (COS) is one of the major sources of stratospheric sulfate aerosols, which affect the global radiation balance and ozone depletion. COS-degrading microorganisms are ubiquitous in soil and important for the global flux of COS. We examined the sulfur isotopic fractionation during the enzymatic degradation of COS by carbonyl sulfide hydrolase (COSase) from Thiobacillus thioparus THI115. The isotopic fractionation constant (34ε value) was -2.2±0.2‰. Under experimental conditions performed at parts per million by volume level of COS, the 34ε value for intact cells of T...
December 2, 2017: Microbes and Environments
Hisayuki Mitsui, Kiwamu Minamisawa
The plant symbiotic α-proteobacterium Sinorhizobium meliloti has two RpoH-type sigma factors, RpoH1 and RpoH2. The former induces the synthesis of heat shock proteins and optimizes interactions with the host. Using a Western blot analysis, we examined time course changes in the intracellular contents of these factors upon a temperature upshift. The RpoH1 level was relatively high and constant, suggesting that its regulatory role in the heat shock response is attained through the activation of the pre-existing RpoH1 protein...
December 2, 2017: Microbes and Environments
Hisashi Muto, Yoshihiro Takaki, Miho Hirai, Sayaka Mino, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals...
November 30, 2017: Microbes and Environments
Noriyuki Konishi, Takashi Okubo, Tomoyuki Yamaya, Toshihiko Hayakawa, Kiwamu Minamisawa
Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application...
November 30, 2017: Microbes and Environments
Miho Hirai, Shinro Nishi, Miwako Tsuda, Michinari Sunamura, Yoshihiro Takaki, Takuro Nunoura
Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications...
November 28, 2017: Microbes and Environments
Chol Gyu Lee, Toshiya Iida, Yohei Uwagaki, Yoko Otani, Kazuhiro Nakaho, Moriya Ohkuma
Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics...
November 28, 2017: Microbes and Environments
Adriana Krolicka, Catherine Boccadoro, Mari Mæland Nilsen, Thierry Baussant
The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring...
November 28, 2017: Microbes and Environments
Ki-Seok Yoon, Nga T Nguyen, Kien Trung Tran, Kohsei Tsuji, Seiji Ogo
Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp...
November 23, 2017: Microbes and Environments
Ken-Ichi Kucho, Daiki Tamari, Shintaro Matsuyama, Takeshi Nabekura, Louis S Tisa
Frankia is a representative genus of nitrogen-fixing (N2-fixing) actinobacteria; however, the molecular mechanisms underlying various phenomena such as the differentiation of a N2 fixation-specific structure (vesicle) and the regulation of N2 fixation (nif) genes, have yet to be elucidated in detail. In the present study, we screened hyphal fragments of Frankia casuarinae that were mutagenized by 1-methyl-3-nitro-1-nitrosoguanidine or gamma rays, and isolated 49 candidate N2 fixation mutants. Twelve of these mutants were selected for further study, and their abilities to grow in NH3-deficient (N-) liquid media and their rates of acetylene reduction activities were evaluated...
November 18, 2017: Microbes and Environments
Ethan T Hillman, Hang Lu, Tianming Yao, Cindy H Nakatsu
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem...
November 10, 2017: Microbes and Environments
Reika Isoda, Shintaro Hara, Teemu Tahvanainen, Yasuyuki Hashidoko
Archaeal communities in mineral soils were compared between a boreal forest in Finland and cold-temperate forest in Japan using 16S rRNA gene-targeted high-throughput sequencing. In boreal soils, Thaumarchaeota Group 1.1c archaea predominated and Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were also detected. In temperate soils, Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were dominant members at the subsurface, whereas their dominancy was replaced by Thermoplasmata archaea at the subsoil...
November 7, 2017: Microbes and Environments
Arthur Fernandes Siqueira, Kiwamu Minamisawa, Cristina Sánchez
When soil oxygen levels decrease, some bradyrhizobia use denitrification as an alternative form of respiration. Bradyrhizobium diazoefficiens (nos(+)) completely denitrifies nitrate (NO3(-)) to dinitrogen, whereas B. japonicum (nos(-)) is unable to reduce nitrous oxide to dinitrogen. We found that anaerobic growth with NO3(-) as the electron acceptor was significantly lower in B. japonicum than in B. diazoefficiens, and this was not explained by the absence of nos in B. japonicum. Our results indicate that the reason for the limited growth of B...
November 3, 2017: Microbes and Environments
Nurul Syahirah Shamsol Anuar, Aeyshah Abang Kassim, Motoo Utsumi, Koji Iwamoto, Masafumi Goto, Kazuya Shimizu, Nor'azizi Othman, Zuriati Zakaria, Norio Sugiura, Hirofumi Hara
Geosmin and 2-methylisoborneol (MIB) outbreaks in tropical water bodies, such as Southeast Asia, by actinomycetes have not yet been elucidated in detail. Six Streptomyces isolates from lowland environments in Malaysia were selected and evaluated for their odor production under different temperatures. The gene responsible for the production of geosmin, geoA, was detected in all isolates, while only two isolates harbored tpc, which is responsible for 2-MIB production. This result suggested that geosmin and 2-MIB synthesis pathway genes already existed in the environment in the Tropics of Southeast Asia...
October 31, 2017: Microbes and Environments
Eunju Shin, Simon Mduma, Julius Keyyu, Robert Fyumagwa, Yeonhee Lee
We isolated Enterococcus species that colonized in the African buffalo (Syncerus caffer) in order to investigate their genetic relatedness and antimicrobial susceptibility. A total of 219 isolates were obtained and a 16S rRNA gene sequence analysis showed they were classified into Enterococcus avium, E. casseliflavus, E. faecalis, E. faecium, E. hirae, or E. mundtii. Multilocus sequence typing of E. faecalis and E. faecium isolates indicated that some of the isolates showed an evolutionary distance that was far from the primary founders...
October 28, 2017: Microbes and Environments
Alejandro Villasante, Carolina Ramirez, Natalia Catalán, Jaime Romero
The aim of the present study was to identify major bacteria associated with the swim bladder in the rainbow trout, Oncorhynchus mykiss. We extracted DNA from the swim bladder and gut contents in order to perform a temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S rRNA amplicons for bacterial identification to further compare both profiles. Arthrobacter and Cellulosimicrobium were the major genera observed in the swim bladder in fish, but were not present in fish gut contents; Mycoplasma were instead observed in these samples...
October 14, 2017: Microbes and Environments
Sachi Tanaka, Kana Yamamoto, Chisato Hamajima, Fuka Takahashi, Kazuki Yamada, Kanon Furuya, Yutaka Uyeno
We aimed to investigate the effects of feeding fermented Brassica rapa L. on ecological and immunological changes in the mouse gut using in vitro cultivation tests and in vivo experiments in normal mice. In the preliminary in vitro study, two B. rapa L. products from different fermentation periods (one d [SF] or six months [LF]) were evaluated along with non-fermented vegetables (NF). Among the components of each product, the insoluble fraction resulted in the most prominent change such as a relative increase in butyrate production during a cultivation inoculated with mouse cecum contents...
September 27, 2017: Microbes and Environments
Ana Umpiérrez, Inés Bado, Martín Oliver, Sofía Acquistapace, Analía Etcheverría, Nora Lía Padola, Rafael Vignoli, Pablo Zunino
Escherichia coli is one of the main etiological agents of neonatal calf diarrhea (NCD). The objective of this study was to assess the presence of virulence genes, genetic diversity, and antibiotic resistance mechanisms in E. coli associated with NCD in Uruguay. PCR was used to assess the presence of intimin, Shiga-like toxin, and stable and labile enterotoxin genes. Resistance to fluoroquinolones and oxyimino-cephalosporins was estimated on Müller-Hinton agar plates. Further antibiotic disc-diffusion tests were performed to assess bacterial multi-resistance...
September 27, 2017: Microbes and Environments
Flore Chirila, Alexandra Tabaran, Nicodim Fit, George Nadas, Marian Mihaiu, Flaviu Tabaran, Cornel Cătoi, Oana Lucia Reget, Sorin Daniel Dan
This study was conducted in order to assess the antimicrobial resistance patterns of E. coli isolated from young animals affected between 1980 and 2016. The selected isolates for this study (n=175) carried stx1/stx2 genes and the most prevalent type of pathogenic E. coli found belonged to serogroup O101, antigen (K99)-F41 positive. All STEC-positive isolates were tested for susceptibility to 11 antimicrobials. Multidrug resistance (MDR) increased from 11% during the 1980s to 40% between 2000 and 2016. Resistance to tetracycline and streptomycin was the most frequent co-resistance phenotype (37%)...
September 27, 2017: Microbes and Environments
María Del Rocío Bustillos-Cristales, Ivan Corona-Gutierrez, Miguel Castañeda-Lucio, Carolina Águila-Zempoaltécatl, Eduardo Seynos-García, Ismael Hernández-Lucas, Jesús Muñoz-Rojas, Liliana Medina-Aparicio, Luis Ernesto Fuentes-Ramírez
Methanol-consuming culturable bacteria were isolated from the plant surface, rhizosphere, and inside the stem of Neobuxbaumia macrocephala. All 38 isolates were facultative methylotrophic microorganisms. Their classification included the Classes Actinobacteria, Sphingobacteriia, Alpha-, Beta-, and Gammaproteobacteria. The deduced amino acid sequences of methanol dehydrogenase obtained by PCR belonging to Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria showed high similarity to rare-earth element (REE)-dependent XoxF methanol dehydrogenases, particularly the group XoxF5...
September 27, 2017: Microbes and Environments
Qian-Shan Qin, Ding-Shan Feng, Peng-Fei Liu, Qiao He, Xia Li, Ai-Ming Liu, Hui Zhang, Guo-Quan Hu, Lei Cheng
The methanogenic degradation of hydrocarbons plays an important role in hydrocarbon-contaminated environments in the absence of an external electron acceptor. Members of Syntrophaceae sublineages were previously reported to be responsible for syntrophic alkane degradation. However, limited information is currently available on their physiological capabilities in nature because it is very challenging to cultivate these as-yet uncultured microbes. We herein performed metagenomic sequencing of the methanogenic hexadecane-degrading culture M82 and recovered a nearly complete genome (2...
September 27, 2017: Microbes and Environments
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