journal
https://read.qxmd.com/read/37460325/analysis-of-the-bacterial-flora-of-substrates-used-for-the-cultivation-of-agaricus-bisporus-relationship-between-clostridia-and-yield
#21
JOURNAL ARTICLE
Daishin Tomikawa, Hiroshi Okuda
Agaricus bisporus has a high nutritional value and health benefits and its popularity is increasing among vegans and health-conscious consumers, indicating the need for its stable production. Therefore, we examined the bacterial flora of the substrates used to produce A. bisporus using a 16S rRNA gene ana-lysis and discussed the relationship between the bacterial flora and yield. The results obtained showed that A. bisporus yield slightly decreased with an increase in the abundance of Clostridia in substrates after primary fermentation...
2023: Microbes and Environments
https://read.qxmd.com/read/37438113/high-prevalence-of-pantoea-spp-in-microbiota-associated-with-the-sorghum-plant-bug-stenotus-rubrovittatus-heteroptera-miridae
#22
JOURNAL ARTICLE
Yuto Sato, Tatsuki Akao, Kazutaka Takeshita
The sorghum plant bug, Stenotus rubrovittatus (order Heteroptera: family Miridae), is a notorious insect pest in Japan that causes pecky rice. In the present study, we sampled this insect pest in the northern part of Honshu Island in Japan and investigated its associated microbiota. The results obtained showed that Pantoea dominated the associated microbiota and was the sole genus detected in all samples. The dominant Pantoea were phylogenetically close to rice pathogens. The present results suggest that the sorghum plant bug needs to be regarded and controlled not only as a notorious insect pest, but also as a potential vector of rice pathogenic Pantoea spp...
2023: Microbes and Environments
https://read.qxmd.com/read/37407492/microbiota-in-umbilical-dirt-and-its-relationship-with-odor
#23
JOURNAL ARTICLE
Takehisa Yano, Takao Okajima, Shigeki Tsuchiya, Hisashi Tsujimura
The umbilicus accumulates more dirt than other body surfaces and is difficult to clean. Hygiene in this area is vital, particularly for surgery, because of its proximity to the laparotomy site. Although microorganisms in the umbilicus have been extensively examined, those in umbilical dirt have not due to the lack of an efficient method of collection. We previously established a technique to extract umbilical dirt using the anchor effect of polymers, which are injected into the umbilicus. In the present study, we applied this technique for the first time to investigate umbilical dirt...
2023: Microbes and Environments
https://read.qxmd.com/read/37357389/species-specific-primer-and-probe-sets-for-detection-of-syntrophic-long-chain-fatty-acid-degrading-bacteria-in-anaerobic-digestion-using-quantitative-pcr
#24
JOURNAL ARTICLE
Riku Sakurai, Yasuhiro Fukuda, Chika Tada
Lipid-rich wastes are energy-dense substrates for anaerobic digestion. However, long-chain fatty acids (LCFAs), key intermediates in lipid degradation, inhibit methanogenic activity. In this study, TaqMan-based qPCR assays targeting the 16S rRNA gene of the cardinal LCFA-degrading bacterial species Syntrophomonas palmitatica and S. zehnderi were developed and validated. A trial experiment showed the advantage of species-specific quantification versus genus-specific quantification in assessing bacterial capacity for lipidic waste degradation...
2023: Microbes and Environments
https://read.qxmd.com/read/37344444/light-driven-proton-pumps-as-a-potential-regulator-for-carbon-fixation-in-marine-diatoms
#25
JOURNAL ARTICLE
Susumu Yoshizawa, Tomonori Azuma, Keiichi Kojima, Keisuke Inomura, Masumi Hasegawa, Yosuke Nishimura, Masuzu Kikuchi, Gabrielle Armin, Yuya Tsukamoto, Hideaki Miyashita, Kentaro Ifuku, Takashi Yamano, Adrian Marchetti, Hideya Fukuzawa, Yuki Sudo, Ryoma Kamikawa
Diatoms are a major phytoplankton group responsible for approximately 20% of carbon fixation on Earth. They perform photosynthesis using light-harvesting chlo-rophylls located in plastids, an organelle obtained through eukaryote-eukaryote endosymbiosis. Microbial rhodopsin, a photoreceptor distinct from chlo-rophyll-based photosystems, was recently identified in some diatoms. However, the physiological function of diatom rhodopsin remains unclear. Heterologous expression techniques were herein used to investigate the protein function and subcellular localization of diatom rhodopsin...
2023: Microbes and Environments
https://read.qxmd.com/read/37331792/deep-subseafloor-biogeochemical-processes-and-microbial-populations-potentially-associated-with-the-2011-tohoku-oki-earthquake-at-the-japan-trench-accretionary-wedge-iodp-expedition-343
#26
JOURNAL ARTICLE
Shinsuke Kawagucci, Sanae Sakai, Eiji Tasumi, Miho Hirai, Yoshihiro Takaki, Takuro Nunoura, Masafumi Saitoh, Yuichiro Ueno, Naohiro Yoshida, Takazo Shibuya, James Clifford Sample, Tomoyo Okumura, Ken Takai
Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851‍ ‍m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H2 ) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses...
2023: Microbes and Environments
https://read.qxmd.com/read/37302846/diversity-in-infection-specificity-between-the-bloom-forming-microalga-heterosigma-akashiwo-and-its-dsdna-virus-heterosigma-akashiwo-virus
#27
JOURNAL ARTICLE
Yusaku Funaoka, Haruna Hiromoto, Daichi Morimoto, Michiko Takahashi, Kei Wada, Keizo Nagasaki
Heterosigma akashiwo virus (HaV) is a dsDNA virus that infects the bloom-forming raphidoflagellate Heterosigma akashiwo. Both the host and its virus are phenotypically diverse in terms of infection specificity. Their relationships have been examined based on the occurrence or absence of algal lysis following virus inoculation; however, variations in the strain-level host-virus relationship regarding infectivity and lysis rates remain unclear. Therefore, we performed a series of cross-infectivity tests using 60 H...
2023: Microbes and Environments
https://read.qxmd.com/read/37302844/identification-of-a-novel-gene-involved-in-cell-to-cell-communication-induced-cell-death-and-edna-production-in-streptococcus-mutans
#28
JOURNAL ARTICLE
Ryo Nagasawa, Nobuhiko Nomura, Nozomu Obana
Streptococcus mutans is a major caries-causing bacterium that forms firmly attached biofilms on tooth surfaces. Biofilm formation by S. mutans consists of polysaccharide-dependent and polysaccharide-independent processes. Among polysaccharide-independent processes, extracellular DNA (eDNA) mediates the initial attachment of cells to surfaces. We previously reported that the secreted peptide signal, competence-stimulating peptide (CSP) induced cell death in a subpopulation of cells, leading to autolysis-mediated eDNA release...
2023: Microbes and Environments
https://read.qxmd.com/read/37302843/self-cloning-of-the-catalase-gene-in-environmental-isolates-improves-their-colony-forming-abilities-on-agar-media
#29
JOURNAL ARTICLE
Motoyuki Watanabe, Kensuke Igarashi, Souichiro Kato, Yoichi Kamagata, Wataru Kitagawa
Hydrogen peroxide (H2 O2 ) inhibits microbial growth at a specific concentration. However, we previously isolated two environmental bacterial strains that exhibited sensitivity to a lower H2 O2 concentration in agar plates. Putative catalase genes, which degrade H2 O2 , were detected in their genomes. We herein elucidated the characteristics of these putative genes and their products using a self-cloning technique. The products of the cloned genes were identified as functional catalases. The up-regulation of their expression increased the colony-forming ability of host cells under H2 O2 pressure...
2023: Microbes and Environments
https://read.qxmd.com/read/37286511/genomic-reclassification-and-phenotypic-characterization-of-pseudomonas-putida-strains-deposited-in-japanese-culture-collections
#30
JOURNAL ARTICLE
Tomohiro Morohoshi, Naoya Yaguchi, Nobutaka Someya
Pseudomonas putida is a major species belonging to the genus Pseudomonas. Although several hundred strains of P. putida have been deposited in culture collections, they potentially differ from the genetically defined "true Pseudomonas putida" because many were classified as P. putida based on their phenotypic and metabolic characteristics. A phylogenetic ana-lysis based on the concatenated sequences of the 16S rRNA and rpoD genes revealed that 46 strains of P. putida deposited in Japanese culture collections were classified into nine operational taxonomic units (OTUs) and eleven singletons...
2023: Microbes and Environments
https://read.qxmd.com/read/37225521/effects-of-phosphate-solubilizing-bacteria-on-soil-phosphorus-fractions-and-supply-to-maize-seedlings-grown-in-lateritic-red-earths-and-cinnamon-soils
#31
JOURNAL ARTICLE
Han Long, Jun Wasaki
Phosphorus (P) is often the limiting factor for plant growth because of its low mobility and availability in soils. Phosphate-solubilizing bacteria (PSB) have been shown to increase the availability of soil P fractions, thereby promoting plant growth. We herein investigated the effects of PSB on P availability in two important Chinese soil types: Lateritic red earths (La) and Cinnamon soils (Ci). We initially isolated 5 PSB strains and assessed their effects on soil P fractions. PSB mainly increased moderately labile P in La and labile P in Ci...
2023: Microbes and Environments
https://read.qxmd.com/read/37164688/phylogeny-and-physiological-diversity-of-cold-adapted-anaerobic-bacteria-isolated-from-rice-field-soil-in-japan
#32
JOURNAL ARTICLE
Sachi Honma, Atsuko Ueki, Akio Ichimura, Kouki Suzuki, Nobuo Kaku, Katsuji Ueki
Cold-adapted or psychrotrophic fermentative anaerobic bacteria were isolated from rice field soil in a temperate area in Japan using anaerobic enrichment cultures incubated at 5°C. Most isolates were obligately anaerobic, spore-forming rods and affiliated with different lineages of the genus Clostridium based on 16S rRNA gene sequences. The growth temperature ranges and physiological properties of three representative clostridial isolates (C5S7, C5S11T , and C5S18) were examined. Strain C5S7 grew at 0°C, but not at 20°C, and was identified as Clostridium estertheticum, a psychrophile isolated from spoiled, vacuum-packed, chilled meat (blown pack spoilage, BPS)...
2023: Microbes and Environments
https://read.qxmd.com/read/37081625/membrane-potential-requiring-succinate-dehydrogenase-constitutes-the-key-to-propionate-oxidation-and-is-unique-to-syntrophic-propionate-oxidizing-bacteria
#33
JOURNAL ARTICLE
Tomoyuki Kosaka, Yuka Tsushima, Yusuke Shiota, Takayuki Ishiguchi, Kazuo Matsushita, Minenosuke Matsutani, Mamoru Yamada
Propionate oxidation in Pelotomaculum thermopropionicum is performed under a thermodynamic limit. The most energetically unfavorable reaction in the propionate oxidation pathway is succinate oxidation. Based on previous genomic and transcriptomic ana-lyses, succinate oxidation in P. thermopropionicum under propionate-oxidizing conditions is conducted by the membrane-bound forms of two succinate dehydrogenases (SDHs). We herein examined the activity of SDH, the mechanisms underlying the succinate oxidation reaction in P...
2023: Microbes and Environments
https://read.qxmd.com/read/37045749/unique-rhizobial-communities-dominated-by-bradyrhizobium-liaoningense-and-bradyrhizobium-ottawaense-were-found-in-vegetable-soybean-nodules-in-osaka-prefecture-japan
#34
JOURNAL ARTICLE
Chikage Minakata, Sawa Wasai-Hara, Satori Fujioka, Shuji Sano, Atsushi Matsumura
Vegetable soybean (Glycine max [L.]) is mainly consumed in Asian countries, but has recently attracted attention worldwide due to its high nutritional value. We aimed to identify the indigenous rhizobia of vegetable soybean in Yao City, Osaka Prefecture, Japan, and to clarify the relationships between the rhizobial community and soil environmental factors. Soil samples were collected from 12 vegetable soybean cultivation fields under two different conditions (six greenhouses and six open fields) in Yao City with different varieties of vegetable soybean...
2023: Microbes and Environments
https://read.qxmd.com/read/36948629/novel-insights-into-microbial-behavior-gleaned-using-microfluidics
#35
JOURNAL ARTICLE
Kohei Takahashi, Xiaojie Li, Tatsuki Kunoh, Ryo Nagasawa, Norio Takeshita, Andrew S Utada
Microorganisms develop into communities in nearly every environmental niche, which is typically replete with micrometer-scale gaps and features. In each of these habitats, microorganisms adapt to and are affected by their physical environment. Conventional culture methods use glass bottom dishes or millimeter-scale flow cells, which poorly mimic the complexity of natural micrometer-scale environments; therefore, the limitations associated with the creation of microbe-scale environments with granularity hinder the ability to examine their ecological behavior...
2023: Microbes and Environments
https://read.qxmd.com/read/36935122/insights-into-antifungal-mechanisms-of-bacillus-velezensis-s141-against-cercospora-leaf-spot-in-mungbean-v-radiata
#36
JOURNAL ARTICLE
Pongpan Songwattana, Pakpoom Boonchuen, Pongdet Piromyou, Jenjira Wongdee, Teerana Greetatorn, Sukanya Inthaisong, Piyada Alisha Tantasawat, Kamonluck Teamtisong, Panlada Tittabutr, Nantakorn Boonkerd, Neung Teaumroong
Cercospora leaf spot (CLS) is caused by Cercospora canescens and is one of the most important diseases of mungbean (Vigna radiata). Cercospora leaf spot may result in economic loss in production areas. The present study investigated the potential of Bacillus velezensis S141 as a biocontrol agent for C. canescens PAK1 growth on culture plates. Cell-free secretions from a dual culture of S141+PAK1 inhibited fungal growth more than those from a single culture of S141. The biocontrol efficiency of S141 against Cercospora leaf spot on mungbean was then evaluated by spraying...
2023: Microbes and Environments
https://read.qxmd.com/read/36928278/a-fast-and-easy-method-to-co-extract-dna-and-rna-from-an-environmental-microbial-sample
#37
JOURNAL ARTICLE
Yusuke Okazaki, Tuyen Thi Nguyen, Arisa Nishihara, Hisashi Endo, Hiroyuki Ogata, Shin-Ichi Nakano, Hideyuki Tamaki
We herein propose a fast and easy DNA and RNA co-extraction method for environmental microbial samples. It combines bead beating and phenol-chloroform phase separation followed by the separation and purification of DNA and RNA using the Qiagen AllPrep DNA/RNA mini kit. With a handling time of ~3 h, our method simultaneously extracted high-quality DNA (peak size >10-15‍ ‍kb) and RNA (RNA integrity number >6) from lake bacterioplankton filtered samples. The method is also applicable to low-biomass samples (expected DNA or RNA yield <50‍ ‍ng) and eukaryotic microbial samples, providing an easy option for more versatile eco-genomic applications...
2023: Microbes and Environments
https://read.qxmd.com/read/36878600/transcriptome-and-deletion-mutant-analyses-revealed-that-an-rpoh-family-sigma-factor-is-essential-for-photosystem-production-in-roseateles-depolymerans-under-carbon-starvation
#38
JOURNAL ARTICLE
Tetsushi Suyama, Nanako Kanno, Satoko Matsukura, Kotaro Chihara, Naohiro Noda, Satoshi Hanada
Roseateles depolymerans is an obligately aerobic bacterium that produces a photosynthetic apparatus only under the scarcity of carbon substrates. We herein examined changes in the transcriptomes of R. depolymerans cells to clarify the expression of photosynthesis genes and their upstream regulatory factors under carbon starvation. Transcriptomes 0, 1, and 6‍ ‍h after the depletion of a carbon substrate indicated that transcripts showing the greatest variations (a 500-fold increase [6 h/0 h]) were light-harvesting proteins (PufA and PufB)...
2023: Microbes and Environments
https://read.qxmd.com/read/36858534/the-first-identification-of-a-narnavirus-in-bigyra-a-marine-protist
#39
JOURNAL ARTICLE
Yuto Chiba, Akinori Yabuki, Yoshihiro Takaki, Takuro Nunoura, Syun-Ichi Urayama, Daisuke Hagiwara
Current information on the diversity and evolution of eukaryotic RNA viruses is biased towards host lineages, such as animals, plants, and fungi. Although protists represent the majority of eukaryotic diversity, our understanding of the protist RNA virosphere is still limited. To reveal untapped RNA viral diversity, we screened RNA viruses from 30 marine protist isolates and identified a novel RNA virus named Haloplacidia narnavirus 1 (HpNV1). A phylogenetic ana-lysis revealed that HpNV1 is a new member of the family Narnaviridae...
2023: Microbes and Environments
https://read.qxmd.com/read/36858533/nad-synthetase-is-required-for-free-living-and-symbiotic-nitrogen-fixation-in-the-actinobacterium-frankia-casuarinae
#40
JOURNAL ARTICLE
Ken-Ichi Kucho, Koya Asukai, Thanh Van Nguyen
Frankia spp. are multicellular actinobacteria that fix atmospheric dinitrogen (N2 ) not only in the free-living state, but also in root-nodule symbioses with more than 200 plant species, called actinorhizal plants. To identify novel Frankia genes involved in N2 fixation, we previously isolated mutants of Frankia casuarinae that cannot fix N2 . One of these genes, mutant N3H4, did not induce nodulation when inoculated into the host plant Casuarina glauca. Cell lineages that regained the ability to fix N2 as free-living cells were isolated from the mutant cell population...
2023: Microbes and Environments
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