journal
https://read.qxmd.com/read/38522927/global-distribution-and-diversity-of-marine-parmales
#1
JOURNAL ARTICLE
Hiroki Ban, Hisashi Endo, Akira Kuwata, Hiroyuki Ogata
Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, which exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies on Parmales have been performed; however, their global distribution has not yet been examined in detail. We herein compiled more than 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution...
2024: Microbes and Environments
https://read.qxmd.com/read/38508742/digalign-versatile-and-interactive-visualization-of-sequence-alignment-for-comparative-genomics
#2
JOURNAL ARTICLE
Yosuke Nishimura, Kohei Yamada, Yusuke Okazaki, Hiroyuki Ogata
With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), a web server that provides versatile functionality for comparative genomics with an intuitive interface. It allows the user to perform the highly customizable visualization of a synteny map by simply uploading nucleotide sequences of interest, ranging from a specific region to the whole genome landscape of microorganisms and viruses...
2024: Microbes and Environments
https://read.qxmd.com/read/38447985/gustatory-responsiveness-of-honey-bees-colonized-with-a-defined-or-conventional-gut-microbiota
#3
JOURNAL ARTICLE
Shota Suenami, Masato Sato, Ryo Miyazaki
Gut microbes have many beneficial functions for host animals, such as food digestion and development of the immune system. An increasing number of studies report that gut bacteria also affect host neural function and behavior. The sucrose responsiveness of the western honey bee Apis mellifera, which harbors a characteristic gut microbiota, was recently reported to be increased by the presence of gut microbes. However, this responsiveness may vary depending on the experimental design, as animal behavior may be modulated by physiological states and environmental conditions...
2024: Microbes and Environments
https://read.qxmd.com/read/38104970/a-simple-and-effective-method-for-solid-medium-cultivation-of-strictly-hydrogen-and-sulfur-oxidizing-chemolithoautotrophs-predominant-in-deep-%C3%A2-sea-hydrothermal-fields
#4
JOURNAL ARTICLE
Hisashi Muto, Junichi Miyazaki, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
Strictly hydrogen- and sulfur-oxidizing chemolithoautotrophic bacteria, particularly members of the phyla Campylobacterota and Aquificota, have a cosmopolitan distribution in deep-sea hydrothermal fields. The successful cultivation of these microorganisms in liquid media has provided insights into their physiological, evolutionary, and ecological characteristics. Notably, recent population genetic studies on Sulfurimonas (Campylobacterota) and Persephonella (Aquificota) revealed geographic separation in their populations...
2023: Microbes and Environments
https://read.qxmd.com/read/38092410/diversity-of-the-hydroxylamine-oxidoreductase-hao-gene-and-its-enzyme-active-site-in-agricultural-field-soils
#5
JOURNAL ARTICLE
Tsubasa Ohbayashi, Yong Wang, Luciano Nobuhiro Aoyagi, Shintaro Hara, Kanako Tago, Masahito Hayatsu
Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2 O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2 O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design...
2023: Microbes and Environments
https://read.qxmd.com/read/38092408/transcriptional-regulation-of-methanol-dehydrogenases-in-the-methanotrophic-bacterium-methylococcus-capsulatus-bath-by-soluble-and-insoluble-lanthanides
#6
JOURNAL ARTICLE
Ruoyun Xie, Motoko Takashino, Kensuke Igarashi, Wataru Kitagawa, Souichiro Kato
The effects of soluble and insoluble lanthanides on gene expression in Methylococcus capsulatus Bath were investigated. Genes for lanthanide-containing methanol dehydrogenases (XoxF-MDHs) and their calcium-containing counterparts (MxaFI-MDHs) were up- and down-regulated, respectively, by supplementation with soluble lanthanide chlorides, indicating that M. capsulatus has the "lanthanide switch" observed in other methanotrophs. Insoluble lanthanide oxides also induced the lanthanide switch and were dissolved by the spent medium of M...
2023: Microbes and Environments
https://read.qxmd.com/read/38072409/effects-of-co-existing-heterotrophs-on-physiology-of-and-nitrogen-metabolism-in-autotrophic-nitrite-oxidizing-candidatus-nitrotoga
#7
JOURNAL ARTICLE
Hiroto Ide, Kento Ishii, Yu Takahashi, Hirotsugu Fujitani, Satoshi Tsuneda
Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca...
2023: Microbes and Environments
https://read.qxmd.com/read/38044128/a-novel-rhizobium-sp-chiba-1-strain-exhibits-a-host-range-for-nodule-symbiosis-in-lotus-species
#8
JOURNAL ARTICLE
Yuhei Chiba, Mao Sasaki, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Yasuyuki Kawaharada
Rhizobia are soil bacteria that induce the formation of nodules in the roots of leguminous plants for mutualistic establishment. Although the symbiotic mechanism between Lotus japonicus and its major symbiotic rhizobia, Mesorhizobium loti, has been extensively characterized, our understanding of symbiotic mechanisms, such as host specificity and host ranges, remains limited. In the present study, we isolated a novel Rhizobium strain capable of forming nodules on L. burttii from agricultural soil at Iwate prefecture in Japan...
2023: Microbes and Environments
https://read.qxmd.com/read/37940566/species-specific-microorganisms-in-acid-tolerant-chironomus-larvae-reared-in-a-neutral-ph-range-under-laboratory-conditions-single-dataset-analysis
#9
JOURNAL ARTICLE
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, and Chironomus sulfurosus than for eight acid-sensitive species based on an alpha diversity ana-lysis. The lower evenness observed suggested a biased abundance of microorganisms, which was consistent with the identification of Chironomus species-specific microorganisms (such as Agromyces mediolanus and Comamonas odontotermitis related bacteria) with high abundance in acid-tolerant larvae...
2023: Microbes and Environments
https://read.qxmd.com/read/37914312/bioformulations-derived-from-enterobacter-sp-nrru-n13-and-oligochitosan-alleviate-drought-stress-in-thai-jasmine-rice-oryza-sativa-l-var-kdml105
#10
JOURNAL ARTICLE
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. NRRU-N13, and evaluated the synergistic effects of these bioformulations in combination with different chitosans on the physiological responses of rice under drought stress...
2023: Microbes and Environments
https://read.qxmd.com/read/37866887/cultivation-of-piezotolerant-and-piezophilic-hyperthermophiles-with-a-newly-developed-constant-high-pressure-and-temperature-culturing-and-monitoring-system
#11
JOURNAL ARTICLE
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 cultures. In the present study, we developed a new high temperature and pressure (HTP) incubation system that enabled the maintenance of HT-HHP conditions while sampling incubation medium and mostly eliminated non-biological reactions, including hydrogen generation or the leakage of small gaseous molecules...
2023: Microbes and Environments
https://read.qxmd.com/read/37853632/domain-level-identification-of-single-prokaryotic-cells-by-optical-photothermal-infrared-spectroscopy
#12
JOURNAL ARTICLE
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 of individual bacterial as well as archaeal cells, and the resulting aliphatic CH3 /CH2 intensity ratios showed domain-specific signatures, which may reflect distinctive cellular lipid compositions; however, there was interference by other cellular components...
2023: Microbes and Environments
https://read.qxmd.com/read/37766554/relationship-between-rumen-microbial-composition-and-fibrolytic-isozyme-activity-during-the-biodegradation-of-rice-straw-powder-using-rumen-fluid
#13
JOURNAL ARTICLE
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 byproduct, was ground and used as a substrate. The biodegradation of rice straw powder was performed anaerobically in rumen fluid for 48 h...
2023: Microbes and Environments
https://read.qxmd.com/read/37704450/community-structure-and-predicted-functions-of-actively-growing-bacteria-responsive-to-released-coral-mucus-in-surrounding-seawater
#14
JOURNAL ARTICLE
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 to be elucidated. We herein used a bromodeoxyuridine approach to investigate the structures and functions of bacterial communities growing close to mucus derived from two different Acropora corals, AC1 and AC2...
2023: Microbes and Environments
https://read.qxmd.com/read/37704449/mating-types-of-ustilago-esculenta-infecting-zizania-latifolia-cultivars-in-japan-are-biased-towards-mat-2-and-mat-3
#15
JOURNAL ARTICLE
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 tissue, a PCR-based assessment of the mating type, and in vitro mating experiments. As a result, we obtained heterogametic strains of MAT-2 and MAT-3 as well as MAT-2, but not MAT-3, haploid strains...
2023: Microbes and Environments
https://read.qxmd.com/read/37704435/reactive-sulfur-species-produced-by-cystathionine-%C3%AE-lyase-function-in-the-establishment-of-mesorhizobium-loti-lotus-japonicus-symbiosis
#16
JOURNAL ARTICLE
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 the CSE mutation of M. loti did not affect the early stages of symbiosis, i.e., infection and nodulation, with Lotus japonicus, it reduced the nitrogenase activity of nodules and induced their early senescence...
2023: Microbes and Environments
https://read.qxmd.com/read/37690850/potential-of-predatory-bacteria-to-colonize-the-duckweed-microbiome-and-change-its-structure-a-model-study-using-the-obligate-predatory-bacterium-bacteriovorax-sp-hi3
#17
JOURNAL ARTICLE
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 changed the microbiome structure, which correlated with colonization density. These results reveal that bacterial predatory interactions may be important drivers that shape the duckweed microbiome, suggesting their potential usefulness in modifying the microbiome...
2023: Microbes and Environments
https://read.qxmd.com/read/37661422/particle-attached-microbes-in-eelgrass-vegetation-areas-differ-in-community-structure-depending-on-the-distance-from-the-eelgrass-bed
#18
JOURNAL ARTICLE
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 Is., Mutsu Bay, and Nanao Bay) and inferred the formation and dynamics of suspended particles from a microbial community structure ana-lysis...
2023: Microbes and Environments
https://read.qxmd.com/read/37635077/slight-changes-in-the-gut-microbiome-in-early-stage-chronic-kidney-disease-of-unknown-etiology
#19
JOURNAL ARTICLE
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 in Khon Kaen Province, Thailand. Seventy-two parasite-free participants were distributed among a healthy control group (HC, n=18) and three patient groups (an underlying disease group [UD, n=18], early-stage CKD with underlying disease [CKD-UD, n=18], and early-stage CKD of unknown etiology, [CKDu, n=18])...
2023: Microbes and Environments
https://read.qxmd.com/read/37612118/16s-rrna-gene-sequencing-of-six-psyllid-species-of-the-family-carsidaridae-identified-various-bacteria-including-symbiopectobacterium
#20
JOURNAL ARTICLE
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 gene. The majority of the secondary symbionts identified in the present study were gammaproteobacteria, particularly those of the order Enterobacterales, including Arsenophonus and Sodalis, which are lineages found in a wide variety of insect hosts...
2023: Microbes and Environments
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