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Species-specific Microorganisms in Acid-tolerant Chironomus Larvae Reared in a Neutral pH Range under Laboratory Conditions: Single Dataset Analysis. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Sotaro Fujii,Koichiro Kawai,Yoshihiro Sambongi,Satoshi Wakai
To obtain a more detailed understanding of organismal acid tolerance, the larval microbiomes of 11 Chironomus species collected from acidic or neutral pH areas in Japan and reared at pH 7-8 under laboratory conditions were systematically compared using an amplicon sequencing ana-lysis. Evenness values were lower for the larval microbiomes of acid-tolerant Chironomus cf. riparius, Chironomus fusciceps
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Bioformulations Derived from Enterobacter sp. NRRU-N13 and Oligochitosan Alleviate Drought Stress in Thai Jasmine Rice (Oryza sativa L. var. KDML105). Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Thanakorn Saengsanga,Nutthida Phakratok,Tarntip Rattana
Climate change is predicted to increase the length, severity, and frequency of drought, which limits plant development by changing various physiological and biochemical processes. Therefore, the present study investigated the effects of drought stress on indole-3-acetic and exopolysaccharide production by Enterobacter sp. NRRU-N13, developed bioformulations of plant growth-promoting Enterobacter sp
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Cultivation of Piezotolerant and Piezophilic Hyperthermophiles with a Newly Developed Constant High Pressure and Temperature Culturing and Monitoring System. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Fumiaki Mori,Akira Ijiri,Tomoya Nishimura,Taisuke Wakamatsu,Nozomi Katsuki,Yuki Morono
The Earth's microbial biosphere extends from ambient to extreme environments, including deep-sea hydrothermal vents and subseafloor habitats. Despite efforts to understand the physiological adaptations of these microbes, our knowledge is limited due to the technological challenges associated with reproducing in situ high temperature (HT)-high hydrostatic pressure (HHP) conditions and sampling HT-HHP
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Domain-level Identification of Single Prokaryotic Cells by Optical Photothermal Infrared Spectroscopy. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Motoko Igisu,Masayuki Miyazaki,Sanae Sakai,Satoshi Nakagawa,Hiroyuki D Sakai,Ken Takai
Infrared spectroscopy is used for the chemical characterization of prokaryotes. However, its application has been limited to cell aggregates and lipid extracts because of the relatively low spatial resolution of diffraction. We herein report optical photothermal infrared (O-PTIR) spectroscopy of prokaryotes for a domain-level diagnosis at the single-cell level. The technique provided infrared spectra
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Relationship Between Rumen Microbial Composition and Fibrolytic Isozyme Activity During the Biodegradation of Rice Straw Powder Using Rumen Fluid. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Shuhei Takizawa,Ryoki Asano,Kenichi Abe,Yasuhiro Fukuda,Yasunori Baba,Riku Sakurai,Chika Tada,Yutaka Nakai
Rumen fibrolytic microorganisms have been used to increase the rate of lignocellulosic biomass biodegradation; however, the microbial and isozymatic characteristics of biodegradation remain unclear. Therefore, the present study investigated the relationship between rumen microorganisms and fibrolytic isozymes associated with lignocellulosic biomass hydrolysis. Rice straw, a widely available agricultural
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Community Structure and Predicted Functions of Actively Growing Bacteria Responsive to Released Coral Mucus in Surrounding Seawater. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Akito Taniguchi,Yuki Kuroyanagi,Ryuichiro Aoki,Mitsuru Eguchi
A direct relationship exists between diverse corals and fish farming in Keten Bay, Amami-Oshima, Japan. The release of coral mucus has a significant impact on the microbial activity of surrounding seawater. To obtain a more detailed understanding of biogeochemical cycles in this environment, the effects of coral mucus on the community structure and function of bacteria in surrounding seawater need
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Mating Types of Ustilago esculenta Infecting Zizania latifolia Cultivars in Japan Are Biased towards MAT-2 and MAT-3. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Yuka Chigira,Nobumitsu Sasaki,Ken Komatsu,Kouji Mashimo,Shigeyuki Tanaka,Minori Numamoto,Hiromitsu Moriyama,Takashi Motobayashi
Zizania latifolia cultivars infected by the endophytic fungus Ustilago esculenta develop an edible stem gall. Stem gall development varies among cultivars and individuals and may be affected by the strain of U. esculenta. To isolate haploids from two Z. latifolia cultivars in our paddy fields, Shirakawa and Ittenkou, we herein performed the sporadic isolation of U. esculenta strains from stem gall
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Reactive Sulfur Species Produced by Cystathionine γ-lyase Function in the Establishment of Mesorhizobium loti-Lotus japonicus Symbiosis. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Mitsutaka Fukudome,Haruka Ishizaki,Yuta Shimokawa,Tomoko Mori,Nahoko Uchi-Fukudome,Kamolchanok Umnajkitikorn,Ei-Ichi Murakami,Toshiki Uchiumi,Masayoshi Kawaguchi
Reactive sulfur species (RSS) are present in root nodules; however, their role in symbiosis and the mechanisms underlying their production remain unclear. We herein investigated whether RSS produced by the cystathionine γ-lyase (CSE) of microsymbionts are involved in root nodule symbiosis. A cse mutant of Mesorhizobium loti exhibited the decreased production of hydrogen sulfide and other RSS. Although
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Potential of Predatory Bacteria to Colonize the Duckweed Microbiome and Change Its Structure: A Model Study Using the Obligate Predatory Bacterium, Bacteriovorax sp. HI3. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Daisuke Inoue,So Nakamura,Tomomi Sugiyama,Michihiko Ike
Modifying the duckweed microbiome is a major challenge for enhancing the effectiveness of duckweed-based wastewater treatment and biomass production technologies. We herein examined the potential of the exogenous introduction of predatory bacteria to change the duckweed microbiome. Bacteriovorax sp. HI3, a model predatory bacterium, colonized the core of the Lemna microbiome, and its predatory behavior
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Particle-attached Microbes in Eelgrass Vegetation Areas Differ in Community Structure Depending on the Distance from the Eelgrass Bed. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Md Mehedi Iqbal,Masahiko Nishimura,Masayoshi Sano,Susumu Yoshizawa
Zostera marina (eelgrass) is a submerged flowering plant often found in the coastal areas of Japan. Large amounts of suspended particles form in highly productive environments, such as eelgrass beds, and the behavior of these particles is expected to affect the surrounding microbial community. We investigated the microbial community structure of suspended particles in three eelgrass fields (Ikuno-Shima
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Slight Changes in the Gut Microbiome in Early-stage Chronic Kidney Disease of Unknown Etiology. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Ditsayathan Banjong,Thatsanapong Pongking,Na T D Tran,Somchai Pinlaor,Rungtiwa Dangtakot,Kitti Intuyod,Sirirat Anutrakulchai,Ubon Cha'on,Porntip Pinlaor
Gut dysbiosis and changes in short-chain fatty acids (SCFAs) occur in end-stage chronic kidney disease (CKD); however, the degree of these changes in the gut microbiome and serum SCFA profiles in the early stages of CKD, particularly in CKD of unknown etiology (CKDu), is unclear. We herein investigated the gut microbiome and SCFA profiles of early-stage CKD patients (CKD stages 1-3) in a community
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16S rRNA Gene Sequencing of Six Psyllid Species of the Family Carsidaridae Identified Various Bacteria Including Symbiopectobacterium. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Junnosuke Maruyama,Hiromitsu Inoue,Yuu Hirose,Atsushi Nakabachi
Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that are closely associated with various microbes. To obtain a more detailed understanding of the ecological and evolutionary behaviors of microbes in Psylloidea, the bacterial populations of six psyllid species, belonging to the family Carsidaridae, were analyzed using high-throughput amplicon sequencing of the 16S rRNA
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Analysis of the Bacterial Flora of Substrates Used for the Cultivation of Agaricus bisporus: Relationship between Clostridia and Yield. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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High Prevalence of Pantoea spp. in Microbiota Associated with the Sorghum Plant Bug Stenotus rubrovittatus (Heteroptera: Miridae). Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Microbiota in Umbilical Dirt and Its Relationship with Odor. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Species-specific Primer and Probe Sets for Detection of Syntrophic Long-chain Fatty Acid-degrading Bacteria in Anaerobic Digestion Using Quantitative PCR. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Deep Subseafloor Biogeochemical Processes and Microbial Populations Potentially Associated with the 2011 Tohoku-oki Earthquake at the Japan Trench Accretionary Wedge (IODP Expedition 343). Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Self-cloning of the Catalase Gene in Environmental Isolates Improves Their Colony-forming Abilities on Agar Media. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Motoyuki Watanabe,Kensuke Igarashi,Souichiro Kato,Yoichi Kamagata,Wataru Kitagawa
Hydrogen peroxide (H2O2) inhibits microbial growth at a specific concentration. However, we previously isolated two environmental bacterial strains that exhibited sensitivity to a lower H2O2 concentration in agar plates. Putative catalase genes, which degrade H2O2, were detected in their genomes. We herein elucidated the characteristics of these putative genes and their products using a self-cloning
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Diversity in Infection Specificity between the Bloom-forming Microalga Heterosigma akashiwo and Its dsDNA Virus, Heterosigma akashiwo Virus. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Identification of a Novel Gene Involved in Cell-to-cell Communication-induced Cell Death and eDNA Production in Streptococcus mutans. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Genomic Reclassification and Phenotypic Characterization of Pseudomonas putida Strains Deposited in Japanese Culture Collections. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Effects of Phosphate-solubilizing Bacteria on Soil Phosphorus Fractions and Supply to Maize Seedlings Grown in Lateritic Red Earths and Cinnamon Soils. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Phylogeny and Physiological Diversity of Cold-adapted Anaerobic Bacteria Isolated from Rice Field Soil in Japan. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Membrane Potential-requiring Succinate Dehydrogenase Constitutes the Key to Propionate Oxidation and Is Unique to Syntrophic Propionate-oxidizing Bacteria. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Unique Rhizobial Communities Dominated by Bradyrhizobium liaoningense and Bradyrhizobium ottawaense were Found in Vegetable Soybean Nodules in Osaka Prefecture, Japan. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Novel Insights into Microbial Behavior Gleaned Using Microfluidics. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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;
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Insights into Antifungal Mechanisms of Bacillus velezensis S141 against Cercospora Leaf Spot in Mungbean (V. radiata). Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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A Fast and Easy Method to Co-extract DNA and RNA from an Environmental Microbial Sample. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Transcriptome and Deletion Mutant Analyses Revealed that an RpoH Family Sigma Factor Is Essential for Photosystem Production in Roseateles depolymerans under Carbon Starvation. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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The First Identification of a Narnavirus in Bigyra, a Marine Protist. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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NAD+ Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 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
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Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Seishi Ikeda,Kazuyuki Okazaki,Hiroyuki Takahashi,Hirohito Tsurumaru,Kiwamu Minamisawa
To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September)
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Characterization of Lactic Acid Bacteria from Fermented Fish (pla-paeng-daeng) and Their Cholesterol-lowering and Immunomodulatory Effects. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Engkarat Kingkaew,Hiroshi Konno,Yoshihito Hosaka,Wongsakorn Phongsopitanun,Somboon Tanasupawat
The cholesterol-lowering and immunomodulatory effects and probiotic properties of 25 lactic acid bacteria (LAB) isolated from fermented fish (pla-paeng-daeng) in Thailand were examined in the present study. Based on their phenotypic and genetic characteristics, LAB were identified as Lactiplantibacillus pentosus (Group I, 6 isolates), Lactiplantibacillus argentoratensis (Group II, 1 isolate), Limosilactobacillus
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Diversity and Quantitative Detection of Clade I Type nosZ Denitrifiers in the Arabian Sea Oxygen Minimum Zone. Microbes Environ. (IF 2.2) Pub Date : 2023-01-01 Mandar Bandekar,Nagappa Ramaiah,Seyieleno C Seleyi,Delcy R Nazareth,Jukka Kekäläinen
A significant amount of nitrous oxide (N2O) is effluxed into the atmosphere as a result of marine denitrification in the Arabian Sea (AS) oxygen minimum zone (OMZ). An assessment of temporal variations in the diversity and abundance of nosZ denitrifiers was performed to establish the relative importance of these bacteria in denitrification. Sampling was conducted at the Arabian Sea Time Series (ASTS)
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Delayed Lysis Time at High Multiplicities of Particles in a Chlorovirus-Chlorella Interaction. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Eva J P Lievens,Manuela Spagnuolo,Tom Réveillon,Lutz Becks
When viruses infect microbial cells, their phenotypes depend on the host's genotype and on the environmental conditions. Here we describe such an effect in laboratory strains of the chlorovirus PBCV-1 and its algal host Chlorella variabilis. We studied the growth of six virus isolates, and found that the mean lysis time was 1.34±0.05 times longer at multiplicity of particles (MOP) 10 than at MOP 1
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Mitigation of Paddy Field Soil Methane Emissions by Betaproteobacterium Azoarcus Inoculation of Rice Seeds. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Midori Sakoda,Takeshi Tokida,Yoriko Sakai,Keishi Senoo,Tomoyasu Nishizawa
Paddy fields are a major source of atmospheric methane, a greenhouse gas produced by methanogens and consumed by methanotrophs in flooded soil. The inoculation of rice seeds with the bacterium Azoarcus sp. KH32C alters the rice root-associated soil bacterial community composition. The present study investigated the effects of KH32C-inoculated rice cultivation on soil methanogens and methanotrophs involved
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High-resolution Microbiome Analyses of Nine Psyllid Species of the Family Triozidae Identified Previously Unrecognized but Major Bacterial Populations, including Liberibacter and Wolbachia of Supergroup O. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Atsushi Nakabachi,Hiromitsu Inoue,Yuu Hirose
Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that include important agricultural pests. To obtain insights into the ecological and evolutionary behaviors of microbes, including plant pathogens, in Psylloidea, high-resolution ana-lyses of the microbiomes of nine psyllid species belonging to the family Triozidae were performed using high-throughput amplicon sequencing
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Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Kyohei Kuroda,Kengo Kubota,Shuka Kagemasa,Ryosuke Nakai,Yuga Hirakata,Kyosuke Yamamoto,Masaru K Nobu,Takashi Narihiro
To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached
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Occurrence and Diversity of Listeria monocytogenes Isolated from Two Pig Manure Treatment Plants in France. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Martine Denis,Christine Ziebal,Evelyne Boscher,Sylvie Picard,Morgane Perrot,Meryl Vila Nova,Sophie Roussel,Arnaud Diara,Anne-Marie Pourcher
The presence of Listeria monocytogenes in piggery effluents intended for irrigation crops may be a source of bacterial dissemination in agriculture. The occurrence and diversity of L. monocytogenes in the farm environment were examined in two pig manure treatment systems (S1 and S2). Samples collected over the course of one year consisted of manure, the liquid fraction of treated manure (lagoon effluent)
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Environmental Variables Including Heavy Metals Significantly Shape the Soil Bacterial Community Structure in the Tatun Volcano Group, Northern Taiwan. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 David Anderson,Ying-Ping Song,Yu-Ting Wu
Recent studies suggested the presence of magma chambers from the Tatun volcano group under northern Taiwan's surface, the result of episodic volcanism for 0.2-2.8 million years. However, the microbial community in volcanic soil has not yet been characterized. Therefore, the present study investigated the spatial distribution of microbial communities and their relationships with environmental variables
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Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Yoshiaki Sato,Hiroaki Takebe,Kazato Oishi,Jumpei Yasuda,Hajime Kumagai,Hiroyuki Hirooka,Takashi Yoshida
The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile
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Effects of Marine Sand on the Microbial Degradation of Biodegradable Plastics in Seawater and Biofilm Communities that Formed on Plastic Surfaces. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Tomohiro Morohoshi,Asuka Taniguchi,Ami Sugawara,Tomohiro Suzuki,Shunsuke Sato
Four types of biodegradable plastics were evaluated for their biodegradability in seawater collected at Ajigaura coast, Japan, in the presence or absence of marine sand. One of the plastics, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH), showed a degree of biodegradation in a seawater sample, and the addition of marine sand markedly accelerated its biodegradation. The addition of marine sand
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Nitrite Production by Nitrifying Bacteria in Urban Groundwater Used in a Chlorinated Public Bath System in Japan. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Yu Takahashi,Kento Ishii,Yukie Kikkawa,Kayo Horikiri,Satoshi Tsuneda
In contrast to pathogens, the effects of environmental microbes on the water quality in baths have not yet been examined in detail. We herein focused on a public bath in which groundwater was pumped up as bath water and disinfected by chlorination. Ammonia in groundwater is oxidized to nitrite, thereby reducing residual chlorine. A batch-culture test and bacterial community ana-lysis revealed that
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Evaluation of Disease Suppressiveness of Soils in Croplands by Co-Cultivation of Pathogenic Fusarium oxysporum and Indigenous Soil Microorganisms. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Masahiro Mitsuboshi,Yuuzou Kioka,Katsunori Noguchi,Susumu Asakawa
An evaluation of suppressiveness against soil-borne diseases is important for their control. We herein assessed disease suppression against F. oxysporum f. sp. spinaciae using the Fusarium co-cultivation method in 75 soils collected from croplands around the country. The suppressive effects of soil microbes against F. oxysporum growth were examined by simultaneously culturing soil suspensions and F
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Supplemental Clostridium butyricum MIYAIRI 588 Affects Intestinal Bacterial Composition of Finishing Pigs. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Maki Hirata,Miki Matsuoka,Takuma Hashimoto,Takamichi Oura,Yo Ohnuki,Chika Yoshida,Ayaka Minemura,Daiki Miura,Kentaro Oka,Motomichi Takahashi,Fumiki Morimatsu
Animal gastrointestinal tracts are populated by highly diverse and complex microbiotas. The gut microbiota influences the bioavailability of dietary components and is closely associated with physiological processes in the host. Clostridium butyricum reportedly improves growth performance and affects the gut microbiota and immune functions in post-weaning piglets. However, the effects of C. butyricum
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Simultaneous Nitrogen Removal and Plant Growth Promotion Using Salt-tolerant Denitrifying Bacteria in Agricultural Wastewater. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Huanhuan Zhang,Weishou Shen,Changyi Ma,Shanshan Li,Jie Chen,Xinfei Mou,Wenwen Cheng,Peng Lei,Hong Xu,Nan Gao,Keishi Senoo
Excess nitrate (NO3-) and nitrite (NO2-) in surface waters adversely affect human and environmental health. Bacteria with the ability to remove nitrogen (N) have been isolated to reduce water pollution caused by the excessive use of N fertilizer. To obtain plant growth-promoting rhizobacteria (PGPR) with salt tolerance and NO3--N removal abilities, bacterial strains were isolated from plant rhizosphere
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The Significance of Mycoparasitism by Streptomyces sp. MBCN152-1 for Its Biocontrol Activity against Alternaria brassicicola. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Masafumi Shimizu,Hushna Ara Naznin,Ayaka Hieno
Streptomyces sp. strain MBCN152-1, isolated from cabbage, has potential as a biocontrol agent for Alternaria brassicicola on cabbage seedlings. The present study examined its mode of action. Light microscopy showed that appressorium formation by A. brassicicola was significantly suppressed on cabbage seedlings bacterized with MBCN152-1. Furthermore, scanning electron microscopy revealed that the mycelia
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Modulation of Phytochemicals and Essential Trace Elements in Fruits of Different Tomato Cultivars by the Endophytic Fungus Penicillium pinophilum EU0013. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Sarah Remi Ibiang,Kazunori Sakamoto
The present study investigated the effects of the endophytic fungus, Penicillium pinophilum EU0013 on fruit phytochemical indices and essential trace elements in five tomato cultivars. In a completely randomized design, inoculated and uninoculated seedlings of tomato cultivars (Momotaro, Rodeo, Anaya, Reika, and Cherry) were raised for sixteen weeks in a greenhouse. Fruit fresh weights and root colonization
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An Integrative and Conjugative Element (ICE) Found in Shewanella halifaxensis Isolated from Marine Fish Intestine May Connect Genetic Materials between Human and Marine Environments. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Yuta Sugimoto,Aya Kadoya,Satoru Suzuki
Integrative and conjugative elements (ICEs) play a role in the horizontal transfer of antibiotic resistance genes (ARGs). We herein report an ICE from Shewanella halifaxensis isolated from fish intestine with a similar structure to both a clinical bacterial ICE and marine bacterial plasmid. The ICE was designated ICEShaJpn1, a member of the SXT/R391 family of ICEs (SRIs). ICEShaJpn1 has a common core
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Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea (AOA) from Agricultural Upland Soil. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Huicheng Zhao,Linqi Zhang
Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep
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Intercontinental Diversity of Caballeronia Gut Symbionts in the Conifer Pest Bug Leptoglossus occidentalis. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Tsubasa Ohbayashi,Raynald Cossard,Gaëlle Lextrait,Takahiro Hosokawa,Vincent Lesieur,Kazutaka Takeshita,Kanako Tago,Peter Mergaert,Yoshitomo Kikuchi
Many stinkbugs in the superfamily Coreoidea (Hemiptera: Heteroptera) develop crypts in the posterior midgut, harboring Caballeronia (Burkholderia) symbionts. These symbionts form a monophyletic group in Burkholderia sensu lato, called the "stinkbug-associated beneficial and environmental (SBE)" group, recently reclassified as the new genus Caballeronia. SBE symbionts are separated into the subclades
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Eukaryotic Microbial RNA Viruses-Acute or Persistent? Insights into Their Function in the Aquatic Ecosystem. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Syun-Ichi Urayama,Yoshihiro Takaki,Yuto Chiba,Yanjie Zhao,Misa Kuroki,Daisuke Hagiwara,Takuro Nunoura
Isolated RNA viruses mainly parasitize eukaryotes. RNA viruses either expand horizontally by infecting hosts (acute type) or coexist with the host and are vertically inherited (persistent type). The significance of persistent-type RNA viruses in environmental viromes (the main hosts are expected to be microbes) was only recently reported because they had previously been overlooked in virology. In this
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Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Wipoo Prasitwuttisak,Yuki Hoshiko,Toshinari Maeda,Akira Haraguchi,Katsunori Yanagawa
Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key
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Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Mamoru Oshiki,Yoshihiro Takaki,Miho Hirai,Takuro Nunoura,Atsushi Kamigaito,Satoshi Okabe
Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic ana-lysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus
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Is Habitat More Important than Phylogenetic Relatedness for Elucidating the Gut Bacterial Composition in Sister Lizard Species? Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Mauricio Hernández,Sergio Ancona,Aníbal H Díaz De La Vega-Pérez,Ligia C Muñoz-Arenas,Stephanie E Hereira-Pacheco,Yendi E Navarro-Noya
The gut microbiota influences the phenotype and fitness of a host; however, limited information is currently available on the diversity and functions of the gut microbiota in wild animals. Therefore, we herein examined the diversity, composition, and potential functions of the gut microbiota in three Sceloporus lizards: Sceloporus aeneus, S. bicanthalis, and S. grammicus, inhabiting different habitats
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Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Naoki Fujii,Kyohei Kuroda,Takashi Narihiro,Yoshiteru Aoi,Noriatsu Ozaki,Akiyoshi Ohashi,Tomonori Kindaichi
Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation
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Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Ievgeniia Prekrasna,Mariia Pavlovska,Natalia Miryuta,Artem Dzhulai,Evgen Dykyi,Peter Convey,Iryna Kozeretska,Tymur Bedernichek,Ivan Parnikoza
The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C
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Detection and Characterization of RNA Viruses in Red Macroalgae (Bangiaceae) and Their Food Product (Nori Sheets). Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Yukino Mizutani,Yuto Chiba,Syun-Ichi Urayama,Yuji Tomaru,Daisuke Hagiwara,Kei Kimura
Persistent RNA viruses, which have been suggested to form symbiotic relationships with their hosts, have been reported to occur in eukaryotes, such as plants, fungi, and algae. Based on empirical findings, these viruses may also be present in commercially cultivated macroalgae. Accordingly, the present study aimed to screen red macroalgae (family Bangiaceae conchocelis and Neopyropia yezoensis thallus)
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Symbiosis Contribution of Non-nodulating Bradyrhizobium cosmicum S23321 after Transferal of the Symbiotic Plasmid pDOA9. Microbes Environ. (IF 2.2) Pub Date : 2022-01-01 Dyah Wulandari,Panlada Tittabutr,Pongpan Songwattana,Pongdet Piromyou,Kamonluck Teamtisong,Nantakorn Boonkerd,Pakpoom Boonchuen,Neung Teaumroong
The symbiotic properties of rhizobial bacteria are driven by the horizontal gene transfer of symbiotic genes, which are located in symbiosis islands or on plasmids. The symbiotic megaplasmid pDOA9 of Bradyrhizobium sp. DOA9, carrying the nod, nif, fix, and type three secretion system (T3SS) genes, has been conjugatively transferred to different Bradyrhizobium strains. In the present study, non-nodulating