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Microbes and Environments

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https://www.readbyqxmd.com/read/28592722/release-and-constancy-of-an-antibiotic-resistance-gene-in-seawater-under-grazing-stress-by-ciliates-and-heterotrophic-nanoflagellates
#1
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 8, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28592721/factors-determining-the-biodiversity-of-halophilic-microorganisms-on-historic-masonry-buildings
#2
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 8, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28592720/effect-of-flooding-and-the-nosz-gene-in-bradyrhizobia-on-bradyrhizobial-community-structure-in-the-soil
#3
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 8, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28529264/communities-of-putative-ericoid-mycorrhizal-fungi-isolated-from-alpine-dwarf-shrubs-in-japan-effects-of-host-identity-and-microhabitat
#4
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...
May 20, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28515390/biocontrol-potential-of-an-endophytic-streptomyces-sp-strain-mbcn152-1-against-alternaria-brassicicola-on-cabbage-plug-seedlings
#5
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...
May 18, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28515389/ca-2-in-hybridization-solutions-for-fluorescence-in-situ-hybridization-facilitates-the-detection-of-enterobacteriaceae
#6
Shin Haruta, Takao Iino, Moriya Ohkuma, Ken-Ichiro Suzuki, Yasuo Igarashi
Fluorescence in situ hybridization (FISH) has been employed to identify microorganisms at the single cell level under a microscope. Extensive efforts have been made to improve and extend the FISH technique; however, the development of a widely applicable protocol is a continuing challenge. The present study evaluated the effects of divalent cations in the hybridization solution on the FISH-based detection of various species of bacteria and archaea with rRNA-targeted probes. A flow cytometric analysis after FISH with a standard hybridization buffer detected positive signals from less than 30% of Escherichia coli IAM 1264 cells...
May 18, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28502969/transcription-of-fefe-hydrogenase-genes-during-h2-production-in-clostridium-and-desulfovibrio-spp-isolated-from-a-paddy-field-soil
#7
Ryuko Baba, Mayumi Morita, Susumu Asakawa, Takeshi Watanabe
Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H2 production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H2 production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H2 production rates, whereas those of the others remained unchanged or decreased...
May 13, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28502968/prokaryotic-communities-at-different-depths-between-soils-with-and-without-tomato-bacterial-wilt-but-pathogen-present-in-a-single-greenhouse
#8
Chol Gyu Lee, Toshiya Iida, Yasuhiro Inoue, Yasunori Muramoto, Hideki Watanabe, Kazuhiro Nakaho, Moriya Ohkuma
The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA...
May 13, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28450660/understory-dwarf-bamboo-affects-microbial-community-structures-and-soil-properties-in-a-betula-ermanii-forest-in-northern-japan
#9
Bihe Kong, Lei Chen, Yasuhiro Kasahara, Akihiro Sumida, Kiyomi Ono, Jan Wild, Arata Nagatake, Ryusuke Hatano, Toshihiko Hara
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 properties, including total carbon, total nitrogen, nitrate, and the C:N ratio as well as relative soil moisture. Marked differences were also noted in fungal and bacterial communities between plots...
April 28, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28442658/predominant-but-previously-overlooked-prokaryotic-drivers-of-reductive-nitrogen-transformation-in-paddy-soils-revealed-by-metatranscriptomics
#10
Yoko Masuda, Hideomi Itoh, Yutaka Shiratori, Kazuo Isobe, Shigeto Otsuka, Keishi Senoo
Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies...
April 22, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321009/energy-metabolism-during-anaerobic-methane-oxidation-in-anme-archaea
#11
REVIEW
Shawn E McGlynn
Anaerobic methane oxidation in archaea is often presented to operate via a pathway of "reverse methanogenesis". However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens-in addition to unique terminal reductases-biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing "reverse" thermodynamic potentials...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321008/a-versatile-and-rapidly-deployable-device-to-enable-spatiotemporal-observations-of-the-sessile-microbes-and-environmental-surfaces
#12
Tatsunori Kiyokawa, Ryo Usuba, Nozomu Obana, Masatoshi Yokokawa, Masanori Toyofuku, Hiroaki Suzuki, Nobuhiko Nomura
Although microbes typically associate with surfaces, detailed observations of surface-associated microbes on natural substrata are technically challenging. We herein introduce a flow channel device named the Stickable Flow Device, which is easily configurable and deployable on various surfaces for the microscopic imaging of environmental microbes. We demonstrated the utility of this device by creating a flow channel on different types of surfaces including live leaves. This device enables the real-time imaging of bacterial biofilms and their substrata...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321007/diversity-of-ktedonobacteria-with-actinomycetes-like-morphology-in-terrestrial-environments
#13
Shuhei Yabe, Yasuteru Sakai, Keietsu Abe, Akira Yokota
Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321006/genetic-characterization-of-soybean-rhizobia-isolated-from-different-ecological-zones-in-north-eastern-afghanistan
#14
Safiullah Habibi, Abdul Ghani Ayubi, Naoko Ohkama-Ohtsu, Hitoshi Sekimoto, Tadashi Yokoyama
Seventy rhizobial isolates were obtained from the root nodules of two soybean (Glycine max) cultivars: Japanese cultivar Enrei and USA cultivar Stine3300, which were inoculated with different soil samples from Afghanistan. In order to study the genetic properties of the isolates, the DNA sequences of the 16S rRNA gene and symbiotic genes (nodD1 and nifD) were elucidated. Furthermore, the isolates were inoculated into the roots of two soybean cultivars, and root nodule numbers and nitrogen fixation abilities were subsequently evaluated in order to assess symbiotic performance...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28302989/bacterial-microbiota-associated-with-the-glacier-ice-worm-is-dominated-by-both-worm-specific-and-glacier-derived-facultative-lineages
#15
Takumi Murakami, Takahiro Segawa, Roman Dial, Nozomu Takeuchi, Shiro Kohshima, Yuichi Hongoh
The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28302951/generation-of-small-colony-variants-in-biofilms-by-escherichia-coli-harboring-a-conjugative-f-plasmid
#16
Yosuke Tashiro, Hiroaki Eida, Satoshi Ishii, Hiroyuki Futamata, Satoshi Okabe
A conjugative F plasmid induces mature biofilm formation by Escherichia coli by promoting F-pili-mediated cell-cell interactions and increasing the expression of biofilm-related genes. We herein demonstrated another function for the F plasmid in E. coli biofilms; it contributes to the emergence of genetic and phenotypic variations by spontaneous mutations. Small colony variants (SCVs) were more frequently generated in a continuous flow-cell biofilm than in the planktonic state of E. coli harboring the F plasmid...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28260736/recombinant-sox-enzymes-from-paracoccus-pantotrophus-degrade-hydrogen-sulfide-a-major-component-of-oral-malodor
#17
Atik Ramadhani, Miki Kawada-Matsuo, Hitoshi Komatsuzawa, Takahiko Oho
Hydrogen sulfide (H2S) is emitted from industrial activities, and several chemotrophs possessing Sox enzymes are used for its removal. Oral malodor is a common issue in the dental field and major malodorous components are volatile sulfur compounds (VSCs), including H2S and methyl mercaptan. Paracoccus pantotrophus is an aerobic, neutrophilic facultatively autotrophic bacterium that possesses sulfur-oxidizing (Sox) enzymes in order to use sulfur compounds as an energy source. In the present study, we cloned the Sox enzymes of P...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28260703/streptomyces-cameroonensis-sp-nov-a-geldanamycin-producer-that-promotes-theobroma-cacao-growth
#18
Thaddée Boudjeko, Romaric Armel Mouafo Tchinda, Mina Zitouni, Joëlle Aimée Vera Tchatchou Nana, Sylvain Lerat, Carole Beaulieu
The taxonomy of an actinobacterial strain, designated JJY4(T), was established using a polyphasic approach. JJY4(T) was isolated from the rhizosphere of Chromolaena odorata in Yaoundé (Cameroon) during a project for the selection of biological control agents. Strain JJY4(T) exhibited antimicrobial activities against bacteria, fungi, and oomycetes. Strain JJY4(T) also exhibited the traits of plant growth-promoting rhizobacteria such as the solubilization of inorganic phosphate, production of siderophores and indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase activity...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28239068/complete-genome-sequence-of-pseudomonas-chlororaphis-subsp-aurantiaca-reveals-a-triplicate-quorum-sensing-mechanism-for-regulation-of-phenazine-production
#19
Tomohiro Morohoshi, Takahito Yamaguchi, Xiaonan Xie, Wen-Zhao Wang, Kasumi Takeuchi, Nobutaka Someya
Pseudomonas chlororaphis subsp. aurantiaca StFRB508 regulates phenazine production through N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing. Two sets of AHL-synthase and AHL-receptor genes, phzI/phzR and aurI/aurR, have been identified from the incomplete draft genome of StFRB508. In the present study, the complete genome of StFRB508, comprising a single chromosome of 6,997,933 bp, was sequenced. The complete genome sequence revealed the presence of a third quorum-sensing gene set, designated as csaI/csaR...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28228608/untapped-endophytic-colonization-and-plant-growth-promoting-potential-of-the-genus-novosphingobium-to-optimize-rice-cultivation
#20
Chakrapong Rangjaroen, Rungroch Sungthong, Benjavan Rerkasem, Neung Teaumroong, Rujirek Noisangiam, Saisamorn Lumyong
With the aim of searching for potent diazotrophic bacteria that are free of public health concerns and optimize rice cultivation, the endophytic colonization and plant growth-promoting activities of some endophytic diazotrophic bacteria isolated from rice were evaluated. Among these bacteria, the emerging diazotrophic strains of the genus Novosphingobium effectively associated with rice plant interiors and consequently promoted the growth of rice, even with the lack of a nitrogen source. These results suggest that diazotrophic Novosphingobium is an alternative microbial resource for further development as a safe biological enhancer in the optimization of organic rice cultivation...
March 31, 2017: Microbes and Environments
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