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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
Miho Yoshikawa, Ming Zhang, Koki Toyota
Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs...
September 12, 2017: Microbes and Environments
Kanit Assawatheptawee, Uttapoln Tansawai, Anong Kiddee, Phetrada Thongngen, Phiraphat Punyadi, Tayawee Romgaew, Phattaraporn Kongthai, Tawatchai Sumpradit, Pannika R Niumsup
Sixty-eight cefotaxime-resistant Escherichia coli isolates were recovered from different water environments in Northern Thailand. Isolates were mostly resistant to ceftazidime and aztreonam (>90%). The most common extended-spectrum β-lactamase-encoding gene was blaCTX-M-group 1 (75%) followed by blaCTX-M-group 9 (13.2%). The co-existence of blaCTX-M and AmpC-type β-lactamase genes was detected in 4 isolates (5.9%). Two E. coli isolates carrying blaCTX-M from canal and river water samples belonged to the phylogenetic group B2-ST131, which is known to be pathogenic...
September 9, 2017: Microbes and Environments
Awaluddin Nurmiyanto, Hiroya Kodera, Tomonori Kindaichi, Noriatsu Ozaki, Yoshiteru Aoi, Akiyoshi Ohashi
Candidatus Accumulibacter phosphatis (Accumulibacter), which plays an important role in enhanced biological phosphorus removal in wastewater treatment plants, is phylogenetically classified into two major types (Types I and II). Phosphate concentrations affect the Accumulibacter community of the biomass enriched in treatment plants. Therefore, in the present study, Accumulibacter enrichments were conducted using a down-flow hanging sponge reactor under five conditions and a wide range of controlled phosphate concentrations in order to investigate how phosphate governs the community...
September 9, 2017: Microbes and Environments
Ruizhen Wang, Leiming Dong, Yuequ Chen, Liangjian Qu, Qinghua Wang, Yongan Zhang
Symbioses have played pivotal roles in biological, ecological, and evolutionary diversification. Symbiotic bacteria affect the biology of hosts in a number of ways. Esteya vermicola, an endoparasitic nematophagous fungus, has high infectivity in the pine wood nematode (PWN), which causes devastating ecological damage and economic losses in Asia and Europe. An integration of molecular, phylogenetic, and morphological analyses revealed that surface-sterilized E. vermicola with septate hyphae from different geographic locations harbor bacterial endosymbionts...
August 19, 2017: Microbes and Environments
Iulia Lupan, Rahela Carpa, Andreea Oltean, Beatrice Simona Kelemen, Octavian Popescu
The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county...
August 5, 2017: Microbes and Environments
Hiroki Suga, Sakiko Kikuchi, Yasuo Takeichi, Chihiro Miyamoto, Masaaki Miyahara, Satoshi Mitsunobu, Takuji Ohigashi, Kazuhiko Mase, Kanta Ono, Yoshio Takahashi
Natural bacteriogenic iron oxides (BIOS) were investigated using local-analyzable synchrotron-based scanning transmission X-ray microscopy (STXM) with a submicron-scale resolution. Cell, cell sheath interface (EPS), and sheath in the BIOS were clearly depicted using C-, N-, and O- near edge X-ray absorption fine structure (NEXAFS) obtained through STXM measurements. Fe-NEXAFS obtained from different regions of BIOS indicated that the most dominant iron mineral species was ferrihydrite. Fe(II)- and/or Fe(III)-acidic polysaccharides accompanied ferrihydrite near the cell and EPS regions...
August 5, 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
Gitanjali NandaKafle, Tarren Seale, Toby Flint, Madhav Nepal, Stephanus N Venter, Volker S Brözel
Escherichia coli is widely considered to not survive for extended periods outside the intestines of warm-blooded animals; however, recent studies demonstrated that E. coli strains maintain populations in soil and water without any known fecal contamination. The objective of this study was to investigate whether the niche partitioning of E. coli occurs between cattle and their pasture. We attempted to clarify whether E. coli from bovine feces differs phenotypically and genotypically from isolates maintaining a population in pasture soil over winter...
September 27, 2017: Microbes and Environments
Yasuhiro Tanaka, Hiroaki Matsuzawa, Hideyuki Tamaki, Masahiro Tagawa, Tadashi Toyama, Yoichi Kamagata, Kazuhiro Mori
A number of novel bacteria including members of rarely cultivated phyla, Acidobacteria and Verrucomicrobia, were successfully isolated from the roots of two emergent plants, Iris pseudacorus and Scirpus juncoides, by a simple culturing method. A total of 47.1% (66 strains) for I. pseudacorus and 42.1% (59 strains) for S. juncoides of all isolates (140 strains from each sample) were phylogenetically novel. Furthermore, Acidobacteria and Verrucomicrobia occupied 10.7% (15 strains) and 2.9% (4 strains) of I. pseudacorus isolates, and 2...
July 22, 2017: Microbes and Environments
Léa Girard, Sébastien Peuchet, Pierre Servais, Annabelle Henry, Nadine Charni-Ben-Tabassi, Julia Baudart
A cellular approach combining Direct Viable Counting and Fluorescent In Situ Hybridization using a one-step multiple-probe technique and Solid Phase Cytometry (DVC-FISH-SPC) was developed to monitor total viable vibrios and cover the detection of a large diversity of vibrios. FISH combined three probes in the same assay and targeted sequences located at different positions on the 16S rRNA of Vibrio and Aliivibrio members. We performed a 10-month in situ study to investigate the weekly dynamics of viable vibrios relative to culturable counts at two northwestern Mediterranean coastal sites, and identified the key physicochemical factors for their occurrence in water using a multivariate analysis...
July 19, 2017: Microbes and Environments
Thi Lan Thanh Bien, Ngo Vy Thao, Shin-Ichi Kitamura, Yumiko Obayashi, Satoru Suzuki
Extracellular DNA (exDNA) is released from bacterial cells through various processes. The antibiotic resistance genes (ARGs) coded on exDNA may be horizontally transferred among bacterial communities by natural transformation. We quantitated the released/leaked tetracycline resistance gene, tet(M) over time under grazing stress by ciliates and heterotrophic nanoflagellates (HNFs), and found that extracellular tet(M) (ex-tetM) increased with bacterial grazing. Separate microcosms containing tet(M)-possessing bacteria with ciliates or HNFs were prepared...
June 24, 2017: Microbes and Environments
Anna Otlewska, Justyna Adamiak, Teresa Stryszewska, Stanisław Kańka, Beata Gutarowska
The aim of the present study was to obtain insights into the relationship between the chemical (salt content and pH) and physico-mechanical (humidity and compressive strength) properties of mineral-based materials from historic buildings with salt efflorescence and the growth and biodiversity of halophilic microorganisms. Samples were mainly characterized by pH 6.5-8.5 and a moisture content of between 0.12 and 3.3%. Significant variations were also found in the salt content (sulfates, chlorides, and nitrates) of the materials...
June 24, 2017: Microbes and Environments
Yuichi Saeki, Misato Nakamura, Maria Luisa T Mason, Tsubasa Yano, Sokichi Shiro, Reiko Sameshima-Saito, Manabu Itakura, Kiwamu Minamisawa, Akihiro Yamamoto
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 incubations. All microcosms were inoculated with Bradyrhizobium japonicum USDA6(T), B. japonicum USDA123, and B. elkanii USDA76(T), which do not possess the nosZ gene, and then half received B...
June 24, 2017: Microbes and Environments
Takahiko Koizumi, Kazuhide Nara
Dwarf shrubs of the family Ericaceae are common in arctic and alpine regions. Many of these plants are associated with ericoid mycorrhizal (ERM) fungi, which allow them to take nutrients and water from the soil under harsh environmental conditions and, thus, affect host plant survival. Despite the importance of ERM fungi to alpine plant communities, limited information is available on the effects of microhabitat and host identity on ERM fungal communities. We investigated the communities of putative ERM fungi isolated from five dwarf shrub species (Arcterica nana, Diapensia lapponica, Empetrum nigrum, Loiseleuria procumbens, and Vaccinium vitis-idaea) that co-occur in an alpine region of Japan, with reference to distinct microhabitats provided by large stone pine (Pinus pumila) shrubs (i...
June 24, 2017: Microbes and Environments
Naglaa Hassan, Satoko Nakasuji, Mohsen Mohamed Elsharkawy, Hushna Ara Naznin, Masaharu Kubota, Hammad Ketta, Masafumi Shimizu
In the present study, 77 strains of endophytic actinomycetes isolated from cabbage were screened in order to assess their biocontrol potential against Alternaria brassicicola on cabbage seedlings. In the first and second screening trials, cabbage seedlings pretreated with mycelial suspensions of each isolate were spray-inoculated with A. brassicicola. Strain MBCN152-1, which exhibited the best protection in screening trials and had no adverse effects on seedling growth, was selected for the greenhouse trial...
June 24, 2017: Microbes and Environments
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