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Microbes and Environments

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https://www.readbyqxmd.com/read/29459501/-effects-of-rhizobium-species-living-with-the-dark-septate-endophytic-fungus-veronaeopsis-simplex-on-organic-substrate-utilization-by-the-host
#1
Yong Guo, Yuuto Matsuoka, Tomoyasu Nishizawa, Hiroyuki Ohta, Kazuhiko Narisawa
Bacteria harbored in/on the hyphae of the dark septate endophyte, Veronaeopsis simplex Y34, were identified as a single Rhizobium species by molecular analyses of bacterial 16S rRNA genes, and were successfully isolated from the endophyte. The Rhizobium-cured fungus was prepared thoroughly by an antibiotic treatment, thereby allowing an examination of their effects on organic substrate utilization. Assays with Biolog® FF microplates revealed that the respiration potential for 52.6% of the tested compounds were significantly different between Rhizobium-harboring and -cured fungal hosts, indicating that organic substrate utilization by V...
February 20, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29459499/-long-term-cultivation-and-metagenomics-reveal-ecophysiology-of-previously-uncultivated-thermophiles-involved-in-biogeochemical-nitrogen-cycle
#2
Shingo Kato, Sanae Sakai, Miho Hirai, Eiji Tasumi, Manabu Nishizawa, Katsuhiko Suzuki, Ken Takai
Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification...
February 16, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29459498/-evaluation-of-suppressiveness-of-soils-exhibiting-soil-borne-disease-suppression-after-long-term-application-of-organic-amendments-by-the-co-cultivation-method-of-pathogenic-fusarium-oxysporum-and-indigenous-soil-microorganisms
#3
Masahiro Mitsuboshi, Yuuzou Kioka, Katsunori Noguchi, Susumu Asakawa
Preventive measures against soil-borne diseases need to be implemented before cultivation because very few countermeasures are available after the development of diseases. Some soils suppress soil-borne diseases despite the presence of a high population density of pathogens. If the suppressiveness of soil against soil-borne diseases may be predicted and diagnosed for crop fields, it may be possible to reduce the labor and cost associated with excessive disinfection practices. We herein evaluated the suppressiveness of soils in fields with the long-term application of organic amendments by examining the growth of pathogenic Fusarium oxysporum co-cultivated with indigenous soil microorganisms on agar plates...
February 16, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29415909/-phylogenetic-diversity-and-single-cell-genome-analysis-of-melainabacteria-a-non-photosynthetic-cyanobacterial-group-in-the-termite-gut
#4
Yuniar Devi Utami, Hirokazu Kuwahara, Takumi Murakami, Takahiro Morikawa, Kaito Sugaya, Kumiko Kihara, Masahiro Yuki, Nathan Lo, Pinsurang Deevong, Sasitorn Hasin, Warin Boonriam, Tetsushi Inoue, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh
Termite guts harbor diverse yet-uncultured bacteria, including a non-photosynthetic cyanobacterial group, the class "Melainabacteria". We herein reported the phylogenetic diversity of "Melainabacteria" in the guts of diverse termites and conducted a single-cell genome analysis of a melainabacterium obtained from the gut of the termite Termes propinquus. We performed amplicon sequencing of 16S rRNA genes from the guts of 60 termite and eight cockroach species, and detected melainabacterial sequences in 48 out of the 68 insect species, albeit with low abundances (0...
February 8, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29415903/-infection-unit-density-as-an-index-of-infection-potential-of-arbuscular-mycorrhizal-fungi
#5
Ryo Ohtomo, Yoshihiro Kobae, Sho Morimoto, Norikuni Oka
The effective use of arbuscular mycorrhizal (AM) fungal function to promote host plant phosphate uptake in agricultural practice requires the accurate quantitative evaluation of AM fungal infection potential in field soil or AM fungal inoculation material. The number of infection units (IUs), intraradical fungal structures derived from single root entries formed after a short cultivation period, may reflect the number of propagules in soil when pot soil is completely permeated by the host root. However, the original IU method, in which all AM propagules in a pot are counted, requires the fine tuning of plant growing conditions and is considered to be laborious...
February 6, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29386425/-molecular-characterization-of-the-bacterial-community-in-biofilms-for-degradation-of-poly-3-hydroxybutyrate-co-3-hydroxyhexanoate-films-in-seawater
#6
Tomohiro Morohoshi, Kento Ogata, Tetsuo Okura, Shunsuke Sato
Microplastics are fragmented pieces of plastic in marine environments, and have become a serious environmental issue. However, the dynamics of the biodegradation of plastic in marine environments have not yet been elucidated in detail. Polyhydroxyalkanoates (PHAs) are biodegradable polymers that are synthesized by a wide range of microorganisms. One of the PHA derivatives, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) has flexible material properties and a low melting temperature. After an incubation in seawater samples, a significant amount of biofilms were observed on the surfaces of PHBH films, and some PHBH films were mostly or partially degraded...
February 1, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29367473/-nitrogen-fixation-in-thermophilic-chemosynthetic-microbial-communities-depending-on-hydrogen-sulfate-and-carbon-dioxide
#7
Arisa Nishihara, Shin Haruta, Shawn E McGlynn, Vera Thiel, Katsumi Matsuura
The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72-75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis...
January 24, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29367472/-host-symbiont-cospeciation-of-termite-gut-cellulolytic-protists-of-the-genera-teranympha-and-eucomonympha-and-their-treponema-endosymbionts
#8
Satoko Noda, Daichi Shimizu, Masahiro Yuki, Osamu Kitade, Moriya Ohkuma
Cellulolytic flagellated protists inhabit the hindgut of termites. They are unique and essential to termites and related wood-feeding cockroaches, enabling host feeding on cellulosic matter. Protists of two genera in the family Teranymphidae (phylum Parabasalia), Eucomonympha and Teranympha, are phylogenetically closely related and harbor intracellular endosymbiotic bacteria from the genus Treponema. In order to obtain a clearer understanding of the evolutionary history of this triplex symbiotic relationship, the molecular phylogenies of the three symbiotic partners, the Teranymphidae protists, their Treponema endosymbionts, and their host termites, were inferred and compared...
January 24, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29311429/-efficacy-of-a-simple-formulation-composed-of-nematode-trapping-fungi-and-bidens-pilosa-var-radiata-scherff-aqueous-extracts-bpe-for-controlling-the-southern-root-knot-nematode
#9
Atsushi Ajitomi, Satoshi Taba, Yoshino Ajitomi, Misa Kinjo, Ken-Taro Sekine
We tested a formulation composed of a mixture of Bidens pilosa var. radiata extract (BPE) and nematode-trapping fungi for its effects on Meloidogyne incognita. In earlier evaluations of the effects of plant extracts on the hyphal growth of 5 species of nematode-trapping fungi with different capture organs (traps), the growth of all species was slightly inhibited. However, an investigation on the number of capture organs and nematode-trapping rates revealed that Arthrobotrys dactyloides formed significantly more rings and nematode traps than those of the control...
December 29, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29237993/-eukaryotic-microbiomes-of-membrane-attached-biofilms-in-membrane-bioreactors-analyzed-by-high-throughput-sequencing-and-microscopic-observations
#10
Tomohiro Inaba, Tomoyuki Hori, Yuya Sato, Tomo Aoyagi, Dai Hanajima, Atsushi Ogata, Hiroshi Habe
Limited information is currently available on the contribution of eukaryotes to the reactor performance of membrane bioreactors (MBRs). Using high-throughput Illumina sequencing of 18S rRNA genes and microscopic observations, we investigated eukaryotic microbiomes in membrane-attached biofilms in MBRs treating piggery wastewater. Protozoa preying on bacteria were frequently detected under stable conditions when membrane clogging was suppressed. However, the eukaryotes preying upon protozoa became predominant in biofilms when membrane fouling rapidly progressed...
December 12, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29199215/-isotopic-fractionation-of-sulfur-in-carbonyl-sulfide-by-carbonyl-sulfide-hydrolase-of-thiobacillus-thioparus-thi115
#11
Takahiro Ogawa, Shohei Hattori, Kazuki Kamezaki, Hiromi Kato, Naohiro Yoshida, Yoko Katayama
Carbonyl sulfide (COS) is one of the major sources of stratospheric sulfate aerosols, which affect the global radiation balance and ozone depletion. COS-degrading microorganisms are ubiquitous in soil and important for the global flux of COS. We examined the sulfur isotopic fractionation during the enzymatic degradation of COS by carbonyl sulfide hydrolase (COSase) from Thiobacillus thioparus THI115. The isotopic fractionation constant (34ε value) was -2.2±0.2‰. Under experimental conditions performed at parts per million by volume level of COS, the 34ε value for intact cells of T...
December 2, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29199214/-expression-of-two-rpoh-sigma-factors-in-sinorhizobium-meliloti-upon-heat-shock
#12
Hisayuki Mitsui, Kiwamu Minamisawa
The plant symbiotic α-proteobacterium Sinorhizobium meliloti has two RpoH-type sigma factors, RpoH1 and RpoH2. The former induces the synthesis of heat shock proteins and optimizes interactions with the host. Using a Western blot analysis, we examined time course changes in the intracellular contents of these factors upon a temperature upshift. The RpoH1 level was relatively high and constant, suggesting that its regulatory role in the heat shock response is attained through the activation of the pre-existing RpoH1 protein...
December 2, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29187693/-a-simple-and-efficient-rna-extraction-method-from-deep-sea-hydrothermal-vent-chimney-structures
#13
Hisashi Muto, Yoshihiro Takaki, Miho Hirai, Sayaka Mino, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals...
November 30, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29187692/-nitrate-supply-dependent-shifts-in-communities-of-root-associated-bacteria-in-arabidopsis
#14
Noriyuki Konishi, Takashi Okubo, Tomoyuki Yamaya, Toshihiko Hayakawa, Kiwamu Minamisawa
Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application...
November 30, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29187708/-library-construction-from-subnanogram-dna-for-pelagic-sea-water-and-deep-sea-sediments
#15
Miho Hirai, Shinro Nishi, Miwako Tsuda, Michinari Sunamura, Yoshihiro Takaki, Takuro Nunoura
Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications...
November 28, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29187707/-comparison-of-prokaryotic-and-eukaryotic-communities-in-soil-samples-with-and-without-tomato-bacterial-wilt-collected-from-different-fields
#16
Chol Gyu Lee, Toshiya Iida, Yohei Uwagaki, Yoko Otani, Kazuhiro Nakaho, Moriya Ohkuma
Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics...
November 28, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29187706/-capturing-early-changes-in-the-marine-bacterial-community-as-a-result-of-crude-oil-pollution-in-a-mesocosm-experiment
#17
Adriana Krolicka, Catherine Boccadoro, Mari Mæland Nilsen, Thierry Baussant
The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring...
November 28, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29176306/-nitrogen-fixation-genes-and-nitrogenase-activity-of-the-non-heterocystous-cyanobacterium-thermoleptolyngbya-sp-o-77
#18
Ki-Seok Yoon, Nga T Nguyen, Kien Trung Tran, Kohsei Tsuji, Seiji Ogo
Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp...
November 23, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29151446/-nitrogen-fixation-mutants-of-the-actinobacterium-frankia-casuarinae-cci3
#19
Ken-Ichi Kucho, Daiki Tamari, Shintaro Matsuyama, Takeshi Nabekura, Louis S Tisa
Frankia is a representative genus of nitrogen-fixing (N2-fixing) actinobacteria; however, the molecular mechanisms underlying various phenomena such as the differentiation of a N2 fixation-specific structure (vesicle) and the regulation of N2 fixation (nif) genes, have yet to be elucidated in detail. In the present study, we screened hyphal fragments of Frankia casuarinae that were mutagenized by 1-methyl-3-nitro-1-nitrosoguanidine or gamma rays, and isolated 49 candidate N2 fixation mutants. Twelve of these mutants were selected for further study, and their abilities to grow in NH3-deficient (N-) liquid media and their rates of acetylene reduction activities were evaluated...
November 18, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29129876/-microbial-ecology-along-the-gastrointestinal-tract
#20
Ethan T Hillman, Hang Lu, Tianming Yao, Cindy H Nakatsu
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem...
November 10, 2017: Microbes and Environments
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