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Microbes and Environments

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https://www.readbyqxmd.com/read/29760298/a-newly-designed-primer-revealed-high-phylogenetic-diversity-of-endozoicomonas-in-coral-reefs
#1
Jia-Ho Shiu, Jiun-Yan Ding, Ching-Hung Tseng, Shueh-Ping Lou, Takuma Mezaki, Yu-Ting Wu, Hsiang-Iu Wang, Sen-Lin Tang
Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95...
May 12, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29709896/ureolytic-prokaryotes-in-soil-community-abundance-and-diversity
#2
Mamoru Oshiki, Mitsuru Araki, Yuga Hirakata, Masashi Hatamoto, Takashi Yamaguchi, Nobuo Araki
Although the turnover of urea is a crucial process in nitrogen transformation in soil, limited information is currently available on the abundance and diversity of ureolytic prokaryotes. The abundance and diversity of the soil 16S rRNA gene and ureC (encoding a urease catalytic subunit) were examined in seven soil types using quantitative PCR and amplicon sequencing with Illumina MiSeq. The amplicon sequencing of ureC revealed that the ureolytic community was composed of phylogenetically varied prokaryotes, and we detected 363 to 1,685 species-level ureC operational taxonomic units (OTUs) per soil sample, whereas 5,984 OTUs were site-specific OTUs found in only one of the seven soil types...
April 28, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29709895/importance-of-soil-temperature-for-the-growth-of-temperate-crops-under-a-tropical-climate-and-functional-role-of-soil-microbial-diversity
#3
Nurul Syazwani Ahmad Sabri, Zuriati Zakaria, Shaza Eva Mohamad, A Bakar Jaafar, Hirofumi Hara
A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures...
April 28, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29681561/bacterial-community-in-water-and-air-of-two-sub-alpine-lakes-in-taiwan
#4
Kshitij Tandon, Shan-Hua Yang, Min-Tao Wan, Chia-Chin Yang, Bayanmunkh Baatar, Chih-Yu Chiu, Jeng-Wei Tsai, Wen-Cheng Liu, Sen-Lin Tang
Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time...
April 21, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29553064/presence-of-a-haloarchaeal-halorhodopsin-like-cl-pump-in-marine-bacteria
#5
Yu Nakajima, Takashi Tsukamoto, Yohei Kumagai, Yoshitoshi Ogura, Tetsuya Hayashi, Jaeho Song, Takashi Kikukawa, Makoto Demura, Kazuhiro Kogure, Yuki Sudo, Susumu Yoshizawa
Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+ -pumping rhodopsin (proteorhodopsin: PR), Na+ -pumping rhodopsin (NaR), and Cl- -pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl- pump...
March 16, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29540639/different-metabolomic-responses-to-carbon-starvation-between-light-and-dark-conditions-in-the-purple-photosynthetic-bacterium-rhodopseudomonas-palustris
#6
Nanako Kanno, Katsumi Matsuura, Shin Haruta
Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29540638/comparative-genomic-insights-into-endofungal-lifestyles-of-two-bacterial-endosymbionts-mycoavidus-cysteinexigens-and-burkholderia-rhizoxinica
#7
Dilruba Sharmin, Yong Guo, Tomoyasu Nishizawa, Shoko Ohshima, Yoshinori Sato, Yusuke Takashima, Kazuhiko Narisawa, Hiroyuki Ohta
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T ) and Mycoavidus cysteinexigens (B1-EBT ), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T ...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29491247/differential-distribution-of-salmonella-serovars-and-campylobacter-spp-isolates-in-free-living-crows-and-broiler-chickens-in-aomori-japan
#8
Masashi Okamura, Miyuki Kaneko, Shinjiro Ojima, Hiroki Sano, Junji Shindo, Hiroaki Shirafuji, Satomi Yamamoto, Taishi Tanabe, Yasuhiro Yoshikawa, Dong-Liang Hu
Salmonella and Campylobacter cause foodborne enteritis mainly via the consumption of raw/undercooked contaminated poultry meat and products. Broiler flocks are primarily colonized with these bacteria; however, the underlying etiology remains unclear. The present study was conducted in order to obtain further information on the prevalence and genotypic distribution of Salmonella and Campylobacter in free-living crows and broiler flocks in a region for 2 years, thereby facilitating estimations of the potential risk of transmission of C...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29479006/plant-materials-are-sustainable-substrates-supporting-new-technologies-of-plant-only-based-culture-media-for-in-vitro-culturing-of-the-plant-microbiota
#9
Elhussein F Mourad, Mohamed S Sarhan, Hassan-Sibroe A Daanaa, Mennatullah Abdou, Ahmed T Morsi, Mohamed R Abdelfadeel, Hend Elsawey, Rahma Nemr, Mahmoud El-Tahan, Mervat A Hamza, Mohamed Abbas, Hanan H Youssef, Abdelhadi A Abdelhadi, Wafaa M Amer, Mohamed Fayez, Silke Ruppel, Nabil A Hegazi
In order to improve the culturability and biomass production of rhizobacteria, we previously introduced plant-only-based culture media. We herein attempted to widen the scope of plant materials suitable for the preparation of plant-only-based culture media. We chemically analyzed the refuse of turfgrass, cactus, and clover. They were sufficiently rich to support good in vitro growth by rhizobacteria isolates representing Proteobacteria and Firmicutes. They were also adequate and efficient to produce a cell biomass in liquid batch cultures...
March 29, 2018: Microbes and Environments
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
#10
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...
March 29, 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
#11
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...
March 29, 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
#12
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...
March 29, 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
#13
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...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29415903/infection-unit-density-as-an-index-of-infection-potential-of-arbuscular-mycorrhizal-fungi
#14
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...
March 29, 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
#15
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...
March 29, 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
#16
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...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29367473/-nitrogen-fixation-in-thermophilic-chemosynthetic-microbial-communities-depending-on-hydrogen-sulfate-and-carbon-dioxide
#17
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
#18
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/29593170/plant-associated-microbes-from-rhizobia-to-plant-microbiomes
#19
Sawa Wasai, Kiwamu Minamisawa
No abstract text is available yet for this article.
2018: Microbes and Environments
https://www.readbyqxmd.com/read/29199215/isotopic-fractionation-of-sulfur-in-carbonyl-sulfide-by-carbonyl-sulfide-hydrolase-of-thiobacillus-thioparus-thi115
#20
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 (34 ɛ value) was -2.2±0.2‰. Under experimental conditions performed at parts per million by volume level of COS, the34 ɛ value for intact cells of T...
December 27, 2017: Microbes and Environments
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