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Microbes and Environments

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https://www.readbyqxmd.com/read/28824050/esteya-vermicola-a-nematophagous-fungus-attacking-the-pine-wood-nematode-harbors-a-bacterial-endosymbiont-affiliated-with-gammaproteobacteria
#1
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
https://www.readbyqxmd.com/read/28747587/distribution-of-diverse-escherichia-coli-between-cattle-and-pasture
#2
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...
July 27, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28724850/spatiotemporal-dynamics-of-total-viable-vibrio-spp-in-a-nw-mediterranean-coastal-area
#3
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
https://www.readbyqxmd.com/read/28592722/release-and-constancy-of-an-antibiotic-resistance-gene-in-seawater-under-grazing-stress-by-ciliates-and-heterotrophic-nanoflagellates
#4
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
https://www.readbyqxmd.com/read/28592721/factors-determining-the-biodiversity-of-halophilic-microorganisms-on-historic-masonry-buildings
#5
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
https://www.readbyqxmd.com/read/28592720/effect-of-flooding-and-the-nosz-gene-in-bradyrhizobia-on-bradyrhizobial-community-structure-in-the-soil
#6
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
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
#7
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
https://www.readbyqxmd.com/read/28515390/biocontrol-potential-of-an-endophytic-streptomyces-sp-strain-mbcn152-1-against-alternaria-brassicicola-on-cabbage-plug-seedlings
#8
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
https://www.readbyqxmd.com/read/28515389/ca-2-in-hybridization-solutions-for-fluorescence-in-situ-hybridization-facilitates-the-detection-of-enterobacteriaceae
#9
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...
June 24, 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
#10
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...
June 24, 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
#11
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...
June 24, 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
#12
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...
June 24, 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
#13
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...
June 24, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321010/discovery-and-complete-genome-sequence-of-a-bacteriophage-from-an-obligate-intracellular-symbiont-of-a-cellulolytic-protist-in-the-termite-gut
#14
Ajeng K Pramono, Hirokazu Kuwahara, Takehiko Itoh, Atsushi Toyoda, Akinori Yamada, Yuichi Hongoh
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 "Candidatus Azobacteroides pseudotrichonymphae" phylotype ProJPt-1, which is an obligate intracellular symbiont of the cellulolytic protist Pseudotrichonympha sp. in the gut of the termite Prorhinotermes japonicus...
June 24, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321009/energy-metabolism-during-anaerobic-methane-oxidation-in-anme-archaea
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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