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Vestiges of Adaptation to the Mesophilic Environment in the Genome of Tepiditoga spiralis gen. nov., sp. nov. Microbes Environ. Pub Date : 2020-01-01 Koji Mori,Kenta Sakurai,Akira Hosoyama,Takeshi Kakegawa,Satoshi Hanada
A novel anaerobic heterotrophic strain, designated strain sy52T, was isolated from a hydrothermal chimney at Suiyo Seamount in the Pacific Ocean. A 16S rRNA gene analysis revealed that the strain belonged to the family Petrotogaceae in the phylum Thermotogae. The strain was mesophilic with optimum growth at 48°C and the phylum primarily comprised hyperthermophiles and thermophiles. Strain sy52T possessed
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Anti-bacterial Effects of MnO2 on the Enrichment of Manganese-oxidizing Bacteria in Downflow Hanging Sponge Reactors. Microbes Environ. Pub Date : 2020-01-01 Shuji Matsushita,Takafumi Hiroe,Hiromi Kambara,Ahmad Shoiful,Yoshiteru Aoi,Tomonori Kindaichi,Noriatsu Ozaki,Hiroyuki Imachi,Akiyoshi Ohashi
We focused on the use of abiotic MnO2 to develop reactors for enriching manganese-oxidizing bacteria (MnOB), which may then be used to treat harmful heavy metal-containing wastewater and in the recovery of useful minor metals. Downflow hanging sponge (DHS) reactors were used under aerobic and open conditions to investigate the potential for MnOB enrichment. The results of an experiment that required
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Invention of Artificial Rice Field Soil: A Tool to Study the Effect of Soil Components on the Activity and Community of Microorganisms Involved in Anaerobic Organic Matter Decomposition. Microbes Environ. Pub Date : 2020-01-01 Yu Maeda,Kazumori Mise,Wataru Iwasaki,Akira Watanabe,Susumu Asakawa,Rasit Asiloglu,Jun Murase
Soils are characterized by diverse biotic and abiotic constituents, and this complexity hinders studies on the effects of individual soil components on microorganisms in soil. Although artificial soils have been used to overcome this issue, anoxic soils have not yet been examined. We herein aimed to create artificial soil that reproduces anaerobic methane production by soil from a rice field. Organic
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Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes Environ. Pub Date : 2020-01-01 Samia Quaiyum,Kensuke Igarashi,Takashi Narihiro,Souichiro Kato
Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment
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Stress Tolerance and Symbiotic and Phylogenic Features of Root Nodule Bacteria Associated with Medicago Species in Different Bioclimatic Regions of Tunisia. Microbes Environ. Pub Date : 2020-01-01 Salem Djedidi,Tadashi Yokoyama,Naoko Ohkama-Ohtsu,Chandra Prasad Risal,Chedly Abdelly,Hitoshi Sekimoto
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Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan. Microbes Environ. Pub Date : 2020-01-01 Kosuke Yamamoto,Minenosuke Matsutani,Yuh Shiwa,Taichiro Ishige,Hikaru Sakamoto,Hiromasa Saitoh,Seiya Tsushima
Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes
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Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen. Microbes Environ. Pub Date : 2020-01-01 Lewis M Ward,Woodward W Fischer,Shawn E McGlynn
We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species-here proposed as Candidatus Anthektikosiphon siderophilum-that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary
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Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation. Microbes Environ. Pub Date : 2020-01-01 Teerana Greetatorn,Shun Hashimoto,Taro Maeda,Mitsutaka Fukudome,Pongdet Piromyou,Kamonluck Teamtisong,Panlada Tittabutr,Nantakorn Boonkerd,Masayoshi Kawaguchi,Toshiki Uchiumi,Neung Teaumroong
Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen
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TEMPURA: Database of Growth TEMPeratures of Usual and RAre Prokaryotes. Microbes Environ. Pub Date : 2020-01-01 Yu Sato,Kenji Okano,Hiroyuki Kimura,Kohsuke Honda
Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.org/db/tempura), which contains the minimum, optimum, and
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Diversity of Sulfur-oxidizing Bacteria at the Surface of Cattle Manure Composting Assessed by an Analysis of the Sulfur Oxidation Gene soxB. Microbes Environ. Pub Date : 2020-01-01 Yumi Mori,Chika Tada,Yasuhiro Fukuda,Yutaka Nakai
Sulfur-oxidizing bacterial diversity at the surface of cattle manure was characterized throughout the composting process using a sulfur oxidation gene (soxB) clone library approach. In the mesophilic phase, clones related to the genera Hydrogenophaga and Hydrogenophilus were characteristically detected. In the thermophilic phase, clones related to the genera Hydrogenophaga and Thiohalobacter were predominant
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Comparative Analysis of Microbial Communities in Fronds and Roots of Three Duckweed Species: Spirodela polyrhiza, Lemna minor, and Lemna aequinoctialis. Microbes Environ. Pub Date : 2020-01-01 Tomoki Iwashita,Yasuhiro Tanaka,Hideyuki Tamaki,Yasuko Yoneda,Ayaka Makino,Yuka Tateno,Yan Li,Tadashi Toyama,Yoichi Kamagata,Kazuhiro Mori
The microbial communities inhabiting the fronds of duckweeds have not been investigated in as much detail as those on the roots. We herein examined the microbial communities in three duckweed species using 16S rRNA amplicon sequencing and compared them to those on the roots. The microbial compositions of the fronds were distinct from those of the roots in the three species. Various types of taxonomic
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Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms? Microbes Environ. Pub Date : 2020-01-01 Jiayue Yang,Yongshou Yang,Manami Ishii,Mayuko Nagata,Wanping Aw,Nozomu Obana,Masaru Tomita,Nobuhiko Nomura,Shinji Fukuda
Microbes inhabit various environments, such as soil, water environments, plants, and animals. Humans harbor a complex commensal microbial community in the gastrointestinal tract, which is known as the gut microbiota. The gut microbiota participates not only in various metabolic processes in the human body, it also plays a critical role in host immune responses. Gut microbes that inhabit the intestinal
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Type III Secretion System of Bradyrhizobium sp. SUTN9-2 Obstructs Symbiosis with Lotus spp. Microbes Environ. Pub Date : 2020-01-01 Shun Hashimoto,Kohki Goto,Pongdet Pyromyou,Pongpan Songwattana,Teerana Greetatorn,Panlada Tittabutr,Nantakorn Boonkerd,Neung Teaumroong,Toshiki Uchiumi
The rhizobial type III secretion system secretes effector proteins into host plant cells, which may either promote or inhibit symbiosis with legumes. We herein demonstrated that the type III secretion system of Bradyrhizobium sp. SUTN9-2 obstructed symbiosis with Lotus japonicus Miyakojima, L. japonicus Gifu, and Lotus burttii. A mutant of SUTN9-2 that is unable to secrete effector proteins showed
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EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence in situ Hybridization (FISH) for Environmental Samples. Microbes Environ. Pub Date : 2020-01-01 Yuki Morono,Kengo Kubota,Daisuke Tsukagoshi,Takeshi Terada
Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition
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Characterization of Vesicle Differentiation Mutants of Frankia casuarinae. Microbes Environ. Pub Date : 2020-01-01 Koya Asukai,Ken-Ichi Kucho
The nitrogen-fixing actinobacterium Frankia develops unique multicellular structures called vesicles, which are the site of nitrogen fixation. These vesicles are surrounded by a thick hopanoid lipid envelope that protects nitrogenase against oxygen inactivation. The phenotypes of five mutants that form smaller numbers of vesicles were investigated. The vesicles of these mutants were smaller than those
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Diversity of Antibiotic Biosynthesis Gene-possessing Rhizospheric Fluorescent Pseudomonads in Japan and Their Biocontrol Efficacy. Microbes Environ. Pub Date : 2020-01-01 Nobutaka Someya,Masaharu Kubota,Kasumi Takeuchi,Yusuke Unno,Ryohei Sakuraoka,Tomohiro Morohoshi
More than 3,000 isolates of fluorescent pseudomonads have been collected from plant roots in Japan and screened for the presence of antibiotic-synthesizing genes. In total, 927 hydrogen cyanide (HCN)-, 47 2,4-diacetylphloroglucinol (PHL)-, 6 pyoluteorin (PLT)-, 14 pyrrolnitrin (PRN)-, and 8 phenazine (PHZ)-producing isolates have been detected. A cluster analysis (≥99% identity) identified 10 operational
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Impact of Atrazine Exposure on the Microbial Community Structure in a Brazilian Tropical Latosol Soil. Microbes Environ. Pub Date : 2020-01-01 Ana Flavia Tonelli Fernandes,Ping Wang,Christopher Staley,Jéssica Aparecida Silva Moretto,Lucas Miguel Altarugio,Sarah Chagas Campanharo,Eliana Guedes Stehling,Michael Jay Sadowsky
Atrazine is a triazine herbicide that is widely used to control broadleaf weeds. Its widespread use over the last 50 years has led to the potential contamination of soils, groundwater, rivers, and lakes. Its main route of complete degradation is via biological means, which is carried out by soil microbiota using a 6-step pathway. The aim of the present study was to investigate whether application of
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Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant. Microbes Environ. Pub Date : 2020-01-01 Yuki Tsuchiya,Tatsunori Nakagawa,Reiji Takahashi
Biofilm carriers have been used to remove ammonia in several wastewater treatment plants (WWTPs) in Japan. However, the abundance and species of ammonia oxidizers in the biofilms formed on the surface of carriers in full-scale operational WWTP tanks remain unclear. In the present study, we conducted quantitative PCR and PCR cloning of the amoA genes of ammonia-oxidizing bacteria and archaea (AOB and
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Mutants Disrupted in the Type III Secretion System of Bradyrhizobium elkanii BLY3-8 Overcame Nodulation Restriction by Rj3-genotype Soybean. Microbes Environ. Pub Date : 2020-01-01 Miku Shobudani,Aung Zaw Htwe,Takeo Yamakawa,Matsujiro Ishibashi,Hirohito Tsurumaru
Bradyrhizobium elkanii BLY3-8 does not form nodules on the roots of Rj3-genotype soybean (cultivar D-51). This is a cultivar-specific nodulation restriction. The genes A6X20_40975 and A6X20_41030 in strain BLY3-8 were predicted to encode the transcriptional activator and apparatus of the type III secretion system (T3SS) (the proteins TtsI and RhcJ), respectively. Mutants disrupted in these genes overcame
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Microevolution of Vibrio parahaemolyticus Isolated from Clinical, Acute Hepatopancreatic Necrosis Disease Infecting Shrimps, and Aquatic Production in China. Microbes Environ. Pub Date : 2020-01-01 Yi Lu,Lulu Yang,Jing Meng,Yong Zhao,Yishan Song,Yongheng Zhu,Jie Ou,Yingjie Pan,Haiquan Liu
Vibrio parahaemolyticus is the leading cause of bacteria-associated foodborne diarrheal diseases and specifically causes early mortality syndrome (EMS), which is technically known as acute hepatopancreatic necrosis disease (AHPND), a serious threat to shrimp aquaculture. To investigate the genetic and evolutionary relationships of V. parahaemolyticus in China, 184 isolates from clinical samples (VPC
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Screening and Assessment of Potential Plant Growth-promoting Bacteria Associated with Allium cepa Linn. Microbes Environ. Pub Date : 2020-01-01 Brian Estuardo Samayoa,Fo-Ting Shen,Wei-An Lai,Wen-Ching Chen
Plant growth-promoting bacteria (PGPB) are beneficial microbes that increase plant growth and yield. However, limited information is currently available on PGPB in onion (Allium cepa Linn.). The aims of the present study were to isolate and identify PGPB in onion and examine the effects of isolated PGPB on germination and growth during the vegetative stage in onion, pak choy (Brassica chinensis), and
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Shewanella algae Relatives Capable of Generating Electricity from Acetate Contribute to Coastal-Sediment Microbial Fuel Cells Treating Complex Organic Matter. Microbes Environ. Pub Date : 2020-01-01 Yoshino Inohana,Shohei Katsuya,Ryota Koga,Atsushi Kouzuma,Kazuya Watanabe
To identify exoelectrogens involved in the generation of electricity from complex organic matter in coastal sediment (CS) microbial fuel cells (MFCs), MFCs were inoculated with CS obtained from tidal flats and estuaries in the Tokyo bay and supplemented with starch, peptone, and fish extract as substrates. Power output was dependent on the CS used as inocula and ranged between 100 and 600 mW m-2 (based
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Viral RNA Genomes Identified from Marine Macroalgae and a Diatom. Microbes Environ. Pub Date : 2020-01-01 Yuto Chiba,Yuji Tomaru,Hiromori Shimabukuro,Kei Kimura,Miho Hirai,Yoshihiro Takaki,Daisuke Hagiwara,Takuro Nunoura,Syun-Ichi Urayama
Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further
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Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates. Microbes Environ. Pub Date : 2020-01-01 Hiroaki Takebe,Kento Tominaga,Kentaro Fujiwara,Keigo Yamamoto,Takashi Yoshida
The phytoplanktonic production and prokaryotic consumption of organic matter significantly contribute to marine carbon cycling. Organic matter released from phytoplankton via three processes (exudation of living cells, cell disruption through grazing, and viral lysis) shows distinct chemical properties. We herein investigated the effects of phytoplanktonic whole-cell fractions (WF) (representing cell
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Levels of Periplasmic Nitrate Reductase during Denitrification are Lower in Bradyrhizobium japonicum than in Bradyrhizobium diazoefficiens. Microbes Environ. Pub Date : 2020-01-01 Arthur Fernandes Siqueira,Masayuki Sugawara,Haruka Arashida,Kiwamu Minamisawa,Cristina Sánchez
Soybean plants host endosymbiotic dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Under oxygen-limiting conditions, Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum perform denitrification by sequentially reducing nitrate (NO3-) to nitrous oxide (N2O) or N2. The anaerobic reduction of NO3- to N2O was previously shown to be lower in B. japonicum than in B. diazoefficiens due
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Effects of Increased 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Activity in Bradyrhizobium sp. SUTN9-2 on Mung Bean Symbiosis under Water Deficit Conditions. Microbes Environ. Pub Date : 2020-01-01 Sukanlaya Sarapat,Pongpan Songwattana,Aphakorn Longtonglang,Kamolchanok Umnajkitikorn,Teerayoot Girdthai,Panlada Tittabutr,Nantakorn Boonkerd,Neung Teaumroong
Bacteria exhibiting 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, which inhibits the biosynthesis of ethylene in higher plants, promote plant growth through the degradation of ethylene precursors, such as ACC. ACC deaminase activity in Bradyrhizobium sp. SUTN9-2 was enhanced by genetic engineering and adaptive laboratory evolution (ALE)-based methods. The transferal of a plasmid containing
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A Novel Cold-adapted Methylovulum species, with a High C16:1ω5c Content, Isolated from an Arctic Thermal Spring in Spitsbergen. Microbes Environ. Pub Date : 2020-01-01 Tajul Islam,Øivind Larsen,Nils-Kåre Birkeland
A novel cold-adapted methane-oxidizing bacterium, termed TFB, was isolated from the thermoglacial Arctic karst spring, Trollosen, located in the South Spitsbergen National Park (Norway). The source water is cold and extremely low in phosphate and nitrate. The isolate belongs to the Methylovulum genus of gammaproteobacterial methanotrophs, with the closest phylogenetic affiliation with Methylovulum
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Size Matters: Ultra-small and Filterable Microorganisms in the Environment. Microbes Environ. Pub Date : 2020-01-01 Ryosuke Nakai
Ultra-small microorganisms are ubiquitous in Earth's environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm3, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., "Candidatus Pelagibacter ubique") and freshwater Actinobacteria and Betaproteobacteria, possess highly streamlined
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Aerobic Production of Bacteriochlorophylls in the Filamentous Anoxygenic Photosynthetic Bacterium, Chloroflexus aurantiacus in the Light. Microbes Environ. Pub Date : 2020-01-01 Kazaha Izaki,Shin Haruta
Filamentous anoxygenic photosynthetic bacteria grow by photosynthesis and aerobic respiration. The present study investigated the effects of light and O2 on bacteriochlorophyll contents and the transcription levels of photosynthesis-related genes in Chloroflexus aurantiacus J-10-fl T. Under aerobic conditions, C. aurantiacus produced marked amounts of bacteriochlorophylls in the presence of light,
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Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method. Microbes Environ. Pub Date : 2020-01-01 Hiromi Kato,Takahiro Ogawa,Hiroyuki Ohta,Yoko Katayama
Carbonyl sulfide (COS) is the most abundant sulfur compound in the atmosphere, and, thus, is important in the global sulfur cycle. Soil is a major sink of atmospheric COS and the numerical distribution of soil microorganisms that degrade COS is indispensable for estimating the COS-degrading potential of soil. However, difficulties are associated with counting COS-degrading microorganisms using culture-dependent
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Biofilm Formation by Streptococcus mutans is Enhanced by Indole via the Quorum Sensing Pathway. Microbes Environ. Pub Date : 2020-01-01 Tomohiro Inaba,Nozomu Obana,Hiroshi Habe,Nobuhiko Nomura
Interspecies interactions among oral microorganisms in the pathogenic biofilms causing dental caries have not yet been elucidated in detail. We herein demonstrated that indole and its derivatives induced biofilm formation by Streptococcus mutans. Indole is an intercellular signaling molecule that is produced by oral bacteria other than S. mutans. The amounts of biofilm and extracellular DNA were significantly
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Aposymbiosis of a Burkholderiaceae-Related Endobacterium Impacts on Sexual Reproduction of Its Fungal Host. Microbes Environ. Pub Date : 2020-01-01 Yusuke Takashima,Yousuke Degawa,Tomoyasu Nishizawa,Hiroyuki Ohta,Kazuhiko Narisawa
Bacterial endosymbionts inhabit diverse fungal lineages. Although the number of studies on bacteria is increasing, the mechanisms by which bacteria affect their fungal hosts remain unclear. We herein examined the homothallic isolate, Mortierella sugadairana YTM39, harboring a Burkholderiaceae-related endobacterium, which did not produce sexual spores. We successfully eliminated the bacterium from fungal
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dsRNA-seq Reveals Novel RNA Virus and Virus-Like Putative Complete Genome Sequences from Hymeniacidon sp. Sponge. Microbes Environ. Pub Date : 2020-01-01 Syun-Ichi Urayama,Yoshihiro Takaki,Daisuke Hagiwara,Takuro Nunoura
Invertebrates are a source of previously unknown RNA viruses that fill gaps in the viral phylogenetic tree. Although limited information is currently available on RNA viral diversity in the marine sponge, a primordial multicellular animal that belongs to the phylum Porifera, the marine sponge is one of the well-studied holobiont systems. In the present study, we elucidated the putative complete genome
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Transcriptome Analysis of the Ammonia-Oxidizing Bacterium Nitrosomonas mobilis Ms1 Reveals Division of Labor between Aggregates and Free-living Cells. Microbes Environ. Pub Date : 2020-01-01 Rino Isshiki,Hirotsugu Fujitani,Satoshi Tsuneda
Bacteria change their metabolic states to increase survival by forming aggregates. Ammonia-oxidizing bacteria also form aggregates in response to environmental stresses. Nitrosomonas mobilis, an ammonia-oxidizing bacterium with high stress tolerance, often forms aggregates mainly in wastewater treatment systems. Despite the high frequency of aggregate formation by N. mobilis, its relationship with
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Enzymatic Degradation of p-Nitrophenyl Esters, Polyethylene Terephthalate, Cutin, and Suberin by Sub1, a Suberinase Encoded by the Plant Pathogen Streptomyces scabies. Microbes Environ. Pub Date : 2020-01-01 Raoudha Jabloune,Mario Khalil,Issam E Ben Moussa,Anne-Marie Simao-Beaunoir,Sylvain Lerat,Ryszard Brzezinski,Carole Beaulieu
The genome of Streptomyces scabies, the predominant causal agent of potato common scab, encodes a potential cutinase, the protein Sub1, which was previously shown to be specifically induced in the presence of suberin. The sub1 gene was expressed in Escherichia coli and the recombinant protein Sub1 was purified and characterized. The enzyme was shown to be versatile because it hydrolyzes a number of
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Distribution of the Harmful Bloom-Forming Cyanobacterium, Microcystis aeruginosa, in 88 Freshwater Environments across Japan. Microbes Environ. Pub Date : 2020-01-01 Takafumi Kataoka,Kako Ohbayashi,Yuki Kobayashi,Hiroyuki Takasu,Shin-Ichi Nakano,Ryuji Kondo,Yoshikuni Hodoki
Microcystis aeruginosa was quantitatively surveyed in 88 freshwater environments across Japan within 3 weeks in 2011. In order to clarify the distribution pattern of M. aeruginosa at the intra-species level, three major genotypes, which were defined by 16S-23S rRNA inter-transcribed-spacer (ITS) regions, were selectively detected using quantitative real-time PCR assays. Of the 68 sites at which the
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Lotus Accessions Possess Multiple Checkpoints Triggered by Different Type III Secretion System Effectors of the Wide-Host-Range Symbiont Bradyrhizobium elkanii USDA61. Microbes Environ. Pub Date : 2020-01-01 Shohei Kusakabe,Nahoko Higasitani,Takakazu Kaneko,Michiko Yasuda,Hiroki Miwa,Shin Okazaki,Kazuhiko Saeki,Atsushi Higashitani,Shusei Sato
Bradyrhizobium elkanii, a rhizobium with a relatively wide host range, possesses a functional type III secretion system (T3SS) that is involved in symbiotic incompatibility against Rj4-genotype soybean (Glycine max) and some accessions of mung bean (Vigna radiata). To expand our knowledge on the T3SS-mediated partner selection mechanism in the symbiotic legume-rhizobia association, we inoculated three
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Isolation and Genomic Characterization of a Proteobacterial Methanotroph Requiring Lanthanides. Microbes Environ. Pub Date : 2020-01-01 Souichiro Kato,Motoko Takashino,Kensuke Igarashi,Wataru Kitagawa
Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca2+-dependent. However
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Enrichment of Type I Methanotrophs with nirS Genes of Three Emergent Macrophytes in a Eutrophic Wetland in China. Microbes Environ. Pub Date : 2020-01-01 Ju-Mei Liu,Zhi-Hua Bao,Wei-Wei Cao,Jing-Jing Han,Jun Zhao,Zhen-Zhong Kang,Li-Xin Wang,Ji Zhao
The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334
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Diversity of Methylobacterium spp. in the Rice of the Vietnamese Mekong Delta. Microbes Environ. Pub Date : 2020-01-01 Khoa Lai,Ngoc Thai Nguyen,Hiroki Miwa,Michiko Yasuda,Hiep Huu Nguyen,Shin Okazaki
The Vietnamese Mekong delta is one of the largest rice-producing areas globally. Methylobacterium spp. are persistent colonizers of the rice plant and exert beneficial effects on plant growth and health. Sixty-one Methylobacterium strains belonging to seven species were predominantly isolated from the phyllosphere of rice cultivated in six Mekong delta provinces. Inoculation tests revealed that some
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Persistent Infection of Simian Foamy Virus Derived from the Japanese Macaque Leads to the High-Level Expression of microRNA that Resembles the miR-1 microRNA Precursor Family. Microbes Environ. Pub Date : 2020-01-01 Akira Hashimoto-Gotoh,Koichi Kitao,Takayuki Miyazawa
MicroRNAs (miRNAs) are a group of small non-coding RNAs that suppress the expression of target mRNAs. The seed sequence of miRNA plays a crucial role in recognizing the 3'-untranslated region of the target mRNA. Cells infected with a simian foamy virus (SFV) isolated from an African green monkey (Chlorocebus aethiops) (SFVcae) showed high expression levels of viral miRNAs encoded in the long terminal
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Improved Isolation of Uncultured Anaerobic Bacteria using Medium Prepared with Separate Sterilization of Agar and Phosphate. Microbes Environ. Pub Date : 2020-01-01 Souichiro Kato,Mia Terashima,Ayano Yama,Megumi Sato,Wataru Kitagawa,Kosei Kawasaki,Yoichi Kamagata
We previously demonstrated that a simple modification in the preparation of agar media, i.e., autoclaving phosphate and agar separately (termed the "PS protocol"), improved the culturability of aerobic microorganisms by reducing the generation of reactive oxygen species. We herein investigated the effects of the PS protocol on the cultivation of anaerobic microorganisms using sludge from a wastewater
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Ammonia Oxidation Potentials and Ammonia Oxidizers of Lichen-Moss Vegetated Soils at Two Ice-free Areas in East Antarctica. Microbes Environ. Pub Date : 2020-01-01 Kentaro Hayashi,Yukiko Tanabe,Nobuhide Fujitake,Morimaru Kida,Yong Wang,Masahito Hayatsu,Sakae Kudoh
The maximum ammonia oxidation potential (AOP) of a topsoil in Langhovde, East Antarctica was 22.1±2.4 ng N g-1 dry soil h-1 (2 mM ammonium, 10°C, n=3). This topsoil exhibited twin AOP peaks (1 and 2 mM ammonium) at 10°C, but not at 20°C. Six and ten operational taxonomic units (OTUs) were identified for ammonia-oxidizing bacteria (AOB) and archaea (AOA) amoA, respectively. AOB were classified into
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Transition of the Bacterial Community and Culturable Chitinolytic Bacteria in Chitin-treated Upland Soil: From Streptomyces to Methionine-auxotrophic Lysobacter and Other Genera. Microbes Environ. Pub Date : 2020-01-01 Yukari Iwasaki,Tatsuya Ichino,Akihiro Saito
Chitin amendment is an agricultural management strategy for controlling soil-borne plant disease. We previously reported an exponential decrease in chitin added to incubated upland soil. We herein investigated the transition of the bacterial community structure in chitin-degrading soil samples over time and the characteristics of chitinolytic bacteria in order to elucidate changes in the chitinolytic
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Diversity of Bradyrhizobium in Non-Leguminous Sorghum Plants: B. ottawaense Isolates Unique in Genes for N2O Reductase and Lack of the Type VI Secretion System. Microbes Environ. Pub Date : 2020-01-01 Sawa Wasai-Hara,Shintaro Hara,Takashi Morikawa,Masayuki Sugawara,Hideto Takami,Junich Yoneda,Tsuyoshi Tokunaga,Kiwamu Minamisawa
Diverse members of Bradyrhizobium diazoefficiens, B. japonicum, and B. ottawaense were isolated from the roots of field-grown sorghum plants in Fukushima, and classified into "Rhizobia" with nodulated soybeans, "Free-living diazotrophs", and "Non-diazotrophs" by nitrogen fixation and nodulation assays. Genome analyses revealed that B. ottawaense members possessed genes for N2O reduction, but lacked
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The Potential for CH4 Production by Syntrophic Microbial Communities in Diverse Deep Aquifers Associated with an Accretionary Prism and its Overlying Sedimentary Layers. Microbes Environ. Pub Date : 2020-01-01 Makoto Matsushita,Shugo Ishikawa,Kenta Magara,Yu Sato,Hiroyuki Kimura
Accretionary prisms are thick masses of sedimentary material scraped from the oceanic crust and piled up at convergent plate boundaries found across large regions of the world. Large amounts of anoxic groundwater and natural gas, mainly methane (CH4), are contained in deep aquifers associated with these accretionary prisms. To identify the subsurface environments and potential for CH4 production by
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Phylogenetic Analysis of Symbiotic Bacteria Associated with Two Vigna Species under Different Agro-Ecological Conditions in Venezuela. Microbes Environ. Pub Date : 2020-01-01 María Daniela Artigas Ramírez,Mingrelia España,Sylwia Lewandowska,Kun Yuan,Shin Okazaki,Naoko Ohkama-Ohtsu,Tadashi Yokoyama
Vigna is a genus of legumes cultivated in specific areas of tropical countries. Species in this genus are important crops worldwide. Vigna species are of great agronomic interest in Venezuela because Vigna beans are an excellent alternative to other legumes. However, this type of crop has some cultivation issues due to sensitivity to acidic soils, high temperatures, and salinity stress, which are common
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Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types. Microbes Environ. Pub Date : 2020-01-01 Reiko Fujimura,Yoichi Azegami,Wei Wei,Hiroko Kakuta,Yutaka Shiratori,Nobuhito Ohte,Keishi Senoo,Shigeto Otsuka,Kazuo Isobe
Recent studies demonstrated that phylogenetically more diverse and abundant bacteria and fungi than previously considered are responsible for denitrification in terrestrial environments. We herein examined the effects of land-use types on the community composition of those denitrifying microbes based on their nitrite reductase gene (nirK and nirS) sequences. These genes can be phylogenetically grouped
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Characterization of Rhizobia for the Improvement of Soybean Cultivation at Cold Conditions in Central Europe. Microbes Environ. Pub Date : 2020-01-01 Kun Yuan,Moritz Reckling,Maria Daniela Artigas Ramirez,Salem Djedidi,Izumi Fukuhara,Takuji Ohyama,Tadashi Yokoyama,Sonoko Dorothea Bellingrath-Kimura,Mosab Halwani,Dilfuza Egamberdieva,Naoko Ohkama-Ohtsu
In central Europe, soybean cultivation is gaining increasing importance to reduce protein imports from overseas and make cropping systems more sustainable. In the field, despite the inoculation of soybean with commercial rhizobia, its nodulation is low. In many parts of Europe, limited information is currently available on the genetic diversity of rhizobia and, thus, biological resources for selecting
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Pretreatment of Lignocellulosic Biomass with Cattle Rumen Fluid for Methane Production: Fate of Added Rumen Microbes and Indigenous Microbes of Methane Seed Sludge. Microbes Environ. Pub Date : 2019-11-19 Yasunori Baba,Yu Matsuki,Shuhei Takizawa,Yoshihisa Suyama,Chika Tada,Yasuhiro Fukuda,Masanori Saito,Yutaka Nakai
The pretreatment of lignocellulosic substrates with cattle rumen fluid was successfully developed to increase methane production. In the present study, a 16S rRNA gene-targeted amplicon sequencing approach using the MiSeq platform was applied to elucidate the effects of the rumen fluid treatment on the microbial community structure in laboratory-scale batch methane fermenters. Methane production in
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Campylobacter in an Urban Estuary: Public Health Insights from Occurrence, HeLa Cytotoxicity, and Caco-2 Attachment Cum Invasion. Microbes Environ. Pub Date : 2019-11-16 Mahbubul H Siddiqee,Rebekah Henry,Rhys A Coleman,Ana Deletic,David T McCarthy
Aquatic recreation in urban estuaries worldwide is often restricted by fecal pollution. Variability in the occurrence of fecal pathogens and their differential virulence potentials within these estuaries may result in variable public health risks. To address this hypothesis, Campylobacter were isolated from the Yarra River estuary, Australia and then characterized via HeLa cell cytotoxicity and attachment
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Vertical Distribution and Diversity of Phototrophic Bacteria within a Hot Spring Microbial Mat (Nakabusa Hot Springs, Japan). Microbes Environ. Pub Date : 2019-11-02 Joval N Martinez,Arisa Nishihara,Mads Lichtenberg,Erik Trampe,Shigeru Kawai,Marcus Tank,Michael Kühl,Satoshi Hanada,Vera Thiel
Phototrophic microbial mats are assemblages of vertically layered microbial populations dominated by photosynthetic microorganisms. In order to elucidate the vertical distribution and diversity of phototrophic microorganisms in a hot spring-associated microbial mat in Nakabusa (Japan), we analyzed the 16S rRNA gene amplicon sequences of the microbial mat separated into five depth horizons, and correlated
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Genetic and Biochemical Diversity for N-acylhomoserine Lactone Biosynthesis in the Plant Pathogen Pectobacterium carotovorum subsp. carotovorum. Microbes Environ. Pub Date : 2019-10-31 Tomohiro Morohoshi,Yuto Ogasawara,Xiaonan Xie,Hiroshi Hamamoto,Nobutaka Someya
The plant pathogen Pectobacterium carotovorum subsp. carotovorum (Pcc) regulates the expression of virulence factors by N-acylhomoserine lactone (AHL)-mediated quorum sensing. The LuxI family protein, ExpI, catalyzes AHL biosynthesis in Pcc. The structure of the predominant AHL produced by ExpI differs among Pcc strains, which may be divided into two quorum-sensing classes (QS classes) based on the
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Distribution of SNSs in Mimivirus Genomes and the Classification of Mimiviruses Isolated from Japan. Microbes Environ. Pub Date : 2019-10-22 Motohiro Akashi,Masaharu Takemura
Mimiviruses have been detected in various habitats. Analyses of single nucleotide substitutions (SNSs) have revealed that SNSs are mainly localized on both ends of the mimivirus genome, and mimivirus lineage A has been split into three genotype groups; therefore, mimiviruses may be classified into lineages and genotype groups based on SNSs. We isolated 9 mimiviruses from Japan and analyzed SNSs. These
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Conjugative Gene Transfer between Nourished and Starved Cells of Photobacterium damselae ssp. damselae and Escherichia coli. Microbes Environ. Pub Date : 2019-10-19 Yoshiaki Kohyama,Satoru Suzuki
Horizontal gene transfer (HGT) between bacteria with different habitats and nutritional requirements is important for the spread of antibiotic resistance genes (ARG). The objective of the present study was to clarify the effects of organic matter on HGT between nourished and starved bacteria. We demonstrated that conjugation ability is affected by the nutritional conditions of the cell and environment
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Thiocyanate Degradation by a Highly Enriched Culture of the Neutrophilic Halophile Thiohalobacter sp. Strain FOKN1 from Activated Sludge and Genomic Insights into Thiocyanate Metabolism. Microbes Environ. Pub Date : 2019-10-19 Mamoru Oshiki,Toshikazu Fukushima,Shuichi Kawano,Yasuhiro Kasahara,Junichi Nakagawa
Thiocyanate (SCN-) is harmful to a wide range of organisms, and its removal is essential for environmental protection. A neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter sp. strain FOKN1, was highly enriched (relative abundance; 98.4%) from activated sludge collected from a bioreactor receiving thiocyanate-rich wastewater. The enrichment culture degraded 3.38 mM thiocyanate
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Exploration of Root-associated Bacteria from the Medicinal Plant Platycodon grandiflorum. Microbes Environ. Pub Date : 2019-10-12 Cong-Min Huang,Wen-Ching Chen,Shih-Han Lin,Yu-Ning Wang,Fo-Ting Shen
The present study was performed to investigate root-associated bacteria from Platycodon grandiflorum, a medicinal plant commonly grown in East Asia. Isolates were obtained from the rhizosphere or root interior with various culture media, and phylogenetic analyses were performed based on their 16S rDNA sequences. In consideration of practical applications, traits related to plant growth promotion and
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Homocitrate Synthase Genes of Two Wide-Host-Range Bradyrhizobium Strains are Differently Required for Symbiosis Depending on Host Plants. Microbes Environ. Pub Date : 2019-10-08 Shun Hashimoto,Jenjira Wongdee,Pongpan Songwattana,Teerana Greetatorn,Kohki Goto,Panlada Tittabutr,Nantakorn Boonkerd,Neung Teaumroong,Toshiki Uchiumi
The nifV gene encodes homocitrate synthase, the enzyme that catalyzes the formation of homocitrate, which is essential for arranging the FeMo-cofactor in the catalytic center of nitrogenase. Some host plants, such as Lotus japonicus, supply homocitrate to their symbionts, in this case, Mesorhizobium loti, which lacks nifV. In contrast, Bradyrhizobium ORS285, a symbiont of Aeschynomene cross-inoculation
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PCR-denaturing Gradient Gel Electrophoresis as a Simple Identification Tool of Arbuscular Mycorrhizal Fungal Isolates. Microbes Environ. Pub Date : 2019-09-25 Ryo Ohtomo,Norikuni Oka,Sho Morimoto
Due to their obligate symbiotic nature and lack of long-term storage methods, the strain collection of arbuscular mycorrhizal (AM) fungi requires periodic proliferation using a pot culture with host plants. Therefore, a method to evaluate the purity of proliferated AM fungal cultures is critical for the quality control of their collection. In a simple evaluation of the purity and identity of a proliferated
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Participation of UV-regulated Genes in the Response to Helix-distorting DNA Damage in the Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. Microbes Environ. Pub Date : 2019-09-21 Shoji Suzuki,Norio Kurosawa
Several species of Sulfolobales have been used as model organisms in the study of response mechanisms to ultraviolet (UV) irradiation in hyperthermophilic crenarchaea. To date, the transcriptional responses of genes involved in the initiation of DNA replication, transcriptional regulation, protein phosphorylation, and hypothetical function have been observed in Sulfolobales species after UV irradiation
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