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Microbes and Environments

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https://www.readbyqxmd.com/read/28442658/predominant-but-previously-overlooked-prokaryotic-drivers-of-reductive-nitrogen-transformation-in-paddy-soils-revealed-by-metatranscriptomics
#1
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/28321010/discovery-and-complete-genome-sequence-of-a-bacteriophage-from-an-obligate-intracellular-symbiont-of-a-cellulolytic-protist-in-the-termite-gut
#2
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...
March 17, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28321009/energy-metabolism-during-anaerobic-methane-oxidation-in-anme-archaea
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28190796/growth-and-grazing-kinetics-of-the-facultative-anaerobic-nanoflagellate-suigetsumonas-clinomigrationis
#13
Ryuji Kondo, Takahiko Okamura
The functional and numerical responses of the facultative anaerobic heterotrophic nanoflagellate, Suigetsumonas clinomigrationis NIES-3647 to prey density were examined under oxic and anoxic conditions. S. clinomigrationis grew at temperatures between 10 and 30°C and in the salinity range of 3.9-36.9 psu. The maximum specific growth and ingestion rates of S. clinomigrationis were lower under anoxic conditions than under oxic conditions. Half-saturation constants for the growth of S. clinomigrationis were within or greater than the range of bacterial densities in the water column of Lake Suigetsu, suggesting that its growth rate is limited by bacterial prey densities in natural environments...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28163278/bacterial-compatibility-in-combined-inoculations-enhances-the-growth-of-potato-seedlings
#14
Christine D Santiago, Shogo Yagi, Motoaki Ijima, Tomoya Nashimoto, Maki Sawada, Seishi Ikeda, Kenji Asano, Yoshitake Orikasa, Takuji Ohwada
The compatibility of strains is crucial for formulating bioinoculants that promote plant growth. We herein assessed the compatibility of four potential bioinoculants isolated from potato roots and tubers (Sphingomonas sp. T168, Streptomyces sp. R170, Streptomyces sp. R181, and Methylibium sp. R182) that were co-inoculated in order to improve plant growth. We screened these strains using biochemical tests, and the results obtained showed that R170 had the highest potential as a bioinoculant, as indicated by its significant ability to produce plant growth-promoting substances, its higher tolerance against NaCl (2%) and AlCl3 (0...
March 31, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28367919/differences-in-survivability-under-starvation-conditions-among-four-species-of-purple-nonsulfur-phototrophic-bacteria
#15
Nanako Kanno, Katsumi Matsuura, Shin Haruta
Volume 29, no. 3, Page 326-328, 2014Page 327, Legend for Fig. 1 IncorrectFig. 1. Changes in viability (black line) and ATP levels (gray line) during carbon-starvation conditions. CorrectFig. 1. Changes in viability (gray line) and ATP levels (black line) during carbon-starvation conditions.
2017: Microbes and Environments
https://www.readbyqxmd.com/read/28367918/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#16
Nobutada Kimura, Yoichi Kamagata
Volume 31, no. 4, Page 435-441, 2016Page 435 Year of "Published online" is incorrect. It should be corrected as follows:incorrect: 2015correct: 2016 This correction has been completed on the electronic file of the present paper available at J-STAGE and PMC.The editorial board expresses sincere apology for the misprinting. Microbes and Environments editorial board.
2017: Microbes and Environments
https://www.readbyqxmd.com/read/28367917/genomics-and-metagenomics-in-microbial-ecology-recent-advances-and-challenges
#17
Takashi Narihiro, Yoichi Kamagata
No abstract text is available yet for this article.
2017: Microbes and Environments
https://www.readbyqxmd.com/read/27885197/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#18
Nobutada Kimura, Yoichi Kamagata
A gene coding for a multicopper oxidase (BopA) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. The recombinant BopA protein produced in Escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in the presence of copper, suggesting that BopA is laccase. A bioinformatic analysis of the bopA gene sequence indicated that it has a phylogenetically bacterial origin, possibly derived from a bacterium within the phylum Deinococcus-Thermus...
December 23, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27867160/morphological-and-taxonomic-properties-of-tokyovirus-the-first-marseilleviridae-member-isolated-from-japan
#19
Masaharu Takemura
Members of the Marseilleviridae family are large DNA viruses with icosahedral particle structures that infect Acanthamoeba cells. The first Marseillevirus to be discovered was isolated in 2009. Since then, several other members of the Marseilleviridae family have been reported, including Lausannevirus, Senegalvirus, Cannes 8 virus, Insectomime virus, Tunisvirus, Melbournevirus, Port-Miou virus, and Brazilian Marseillevirus, which have been isolated from Europe, Africa, Australia, and South America. The morphological and genomic properties of a new Marseilleviridae family member, Tokyovirus, discovered in a water/soil sample from a Japanese river in Tokyo, were described in the present study...
December 23, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27867159/culture-dependent-and-independent-identification-of-polyphosphate-accumulating-dechloromonas-spp-predominating-in-a-full-scale-oxidation-ditch-wastewater-treatment-plant
#20
Mia Terashima, Ayano Yama, Megumi Sato, Isao Yumoto, Yoichi Kamagata, Souichiro Kato
The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp...
December 23, 2016: Microbes and Environments
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