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Microbes and Environments

Yasuhiro Tanaka, Hideyuki Tamaki, Kazuya Tanaka, Erina Tozawa, Hiroaki Matsuzawa, Tadashi Toyama, Yoichi Kamagata, Kazuhiro Mori
We herein described a new microbial isolation method using the interaction between the floating aquatic plant, duckweed, and microbes. We harvested microbial cells from Japanese loosestrife roots and co-cultivated these cells with aseptic duckweed using artificial inorganic medium for the plant for four weeks. During the co-cultivation, some duckweeds were collected every week, and the roots were used for microbial isolation using a low-nutrient plate medium. As a result, diverse microbial isolates, the compositions of which differed from those of the original source (Japanese loosestrife root), were obtained when the roots of duckweed were collected after 2 weeks of cultivation...
November 7, 2018: Microbes and Environments
Mariana Grillo-Puertas, Paola Delaporte-Quintana, Raúl Osvaldo Pedraza, Viviana Andrea Rapisarda
Gluconacetobacter diazotrophicus is a plant growth-promoting bacterium that is used as a bioinoculant. Phosphate (Pi) modulates intracellular polyphosphate (polyP) levels in Escherichia coli, affecting cellular fitness and biofilm formation capacity. It currently remains unclear whether environmental Pi modulates polyP levels in G. diazotrophicus to enhance fitness in view of its technological applications. In high Pi media, cells accumulated polyP and degraded it, thereby improving survival, tolerance to environmental stressors, biofilm formation capacity on abiotic and biotic surfaces, and competence as a growth promoter of strawberry plants...
November 7, 2018: Microbes and Environments
Arisa Nishihara, Vera Thiel, Katsumi Matsuura, Shawn E McGlynn, Shin Haruta
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70-86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae...
November 7, 2018: Microbes and Environments
Shingo Kato, Tomoyo Okumura, Katsuyuki Uematsu, Miho Hirai, Koichi Iijima, Akira Usui, Katsuhiko Suzuki
Rock outcrops of aged deep-sea seamounts are generally covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Although the presence of microorganisms in Fe-Mn crusts has been reported, limited information is currently available on intra- and inter-variations in crust microbial communities. Therefore, we collected several Fe-Mn crusts in bathyal and abyssal zones (water depths of 1,150-5,520 m) in the Takuyo-Daigo Seamount in the northwestern Pacific, and examined microbial communities on the crusts using culture-independent molecular and microscopic analyses...
October 30, 2018: Microbes and Environments
Tomo-O Watsuji, Kaori Motoki, Emi Hada, Yukiko Nagai, Yoshihiro Takaki, Asami Yamamoto, Kenji Ueda, Takashi Toyofuku, Hiroyuki Yamamoto, Ken Takai
The hydrothermal vent squat lobster Shinkaia crosnieri Baba & Williams harbors an epibiotic bacterial community, which is numerically and functionally dominated by methanotrophs affiliated with Methylococcaceae and thioautotrophs affiliated with Sulfurovum and Thiotrichaceae. In the present study, shifts in the phylogenetic composition and metabolic function of the epibiont community were investigated using S. crosnieri individuals, which were reared for one year in a tank fed with methane as the energy and carbon source...
October 17, 2018: Microbes and Environments
Syun-Ichi Urayama, Yoshihiro Takaki, Takuro Nunoura, Norio Miyamoto
The deep sea, the largest biosphere on Earth, nurtures a large variety of animals. However, no virus that infects deep-sea animals has been found. We herein report the first full-length RNA viral genome sequence identified from the deep-sea animal, Osedax japonicus, called Osedax japonicus RNA virus 1 (OjRV1). This sequence showed the highest amino acid sequence similarity to a virus of the family Togaviridae. However, the phylogenetic position and genome structure of OjRV1 differed from those of viruses in Togaviridae...
October 13, 2018: Microbes and Environments
Shun Kobayashi, Daisuke Hira, Keitaro Yoshida, Masanori Toyofuku, Yosuke Shida, Wataru Ogasawara, Takashi Yamaguchi, Nobuo Araki, Mamoru Oshiki
Aerobic ammonia-oxidizing archaea (AOA) play a crucial role in the global nitrogen cycle by oxidizing ammonia to nitrite, and nitric oxide (NO) is a key intermediate in AOA for sustaining aerobic ammonia oxidation activity. We herein heterologously expressed the NO-forming, copper-containing, dissimilatory nitrite reductase (NirK) from Nitrososphaera viennensis and investigated its enzymatic properties. The recombinant protein catalyzed the reduction of 15 NO2 - to 15 NO, the oxidation of hydroxylamine (15 NH2 OH) to 15 NO, and the production of 14-15 N2 O from 15 NH2 OH and 14 NO2 - ...
October 12, 2018: Microbes and Environments
Justyna Mazurek, Ewa Bok, Katarzyna Baldy-Chudzik
Antibiotics in animal husbandry are used to maintain welfare, but lead to the generation of resistant strains. We analyzed commensal multidrug-resistant Escherichia coli from pigs at the beginning and end of the production cycle in a farm with a farrow-to-finish system in order to investigate whether clonal spread or horizontal gene transfer constitutes the main factor responsible for the prevalence of resistance in this environment. Among 380 isolates, 56 multidrug-resistant E. coli with a similar resistant phenotype were selected for more detailed investigations including a genomic similarity analysis and the detection of mobile elements...
September 29, 2018: Microbes and Environments
Mohamed S Sarhan, Sascha Patz, Mervat A Hamza, Hanan H Youssef, Elhussein F Mourad, Mohamed Fayez, Brian Murphy, Silke Ruppel, Nabil A Hegazi
The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar)...
September 29, 2018: Microbes and Environments
Kazumori Mise, Kazuki Fujita, Takashi Kunito, Keishi Senoo, Shigeto Otsuka
Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils...
September 29, 2018: Microbes and Environments
Rajani Ghaju Shrestha, Yasuhiro Tanaka, Bikash Malla, Sarmila Tandukar, Dinesh Bhandari, Daisuke Inoue, Kazunari Sei, Jeevan B Sherchand, Eiji Haramoto
Arcobacter spp. are emerging pathogens associated with gastroenteritis in humans. The objective of this study was to develop a highly sensitive and broadly reactive quantitative PCR (qPCR) assay for Arcobacter spp. and to apply the developed assay to different water sources in the Kathmandu Valley, Nepal. Fifteen samples to be analyzed by next-generation sequencing were collected from 13 shallow dug wells, a deep tube well, and a river in the Kathmandu Valley in August 2015. Among the 86 potential pathogenic bacterial genera identified, Acinetobacter, Pseudomonas, Flavobacterium, and Arcobacter were detected with relatively high abundance in 15, 14, 12, and 8 samples, respectively...
September 29, 2018: Microbes and Environments
Tomohiro Morohoshi, Taishiro Oi, Haruna Aiso, Tomohiro Suzuki, Tetsuo Okura, Shunsuke Sato
We investigated biofilm formation on biodegradable plastics in freshwater samples. Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) was covered by a biofilm after an incubation in freshwater samples. A next generation sequencing analysis of the bacterial communities of biofilms that formed on PHBH films revealed the dominance of the order Burkholderiales. Furthermore, Acidovorax and Undibacterium were the predominant genera in most biofilms. Twenty-five out of 28 PHBH-degrading isolates were assigned to the genus Acidovorax, while the other three were assigned to the genera Undibacterium and Chitinimonas...
September 29, 2018: Microbes and Environments
Jeonghwan Jang, Naoaki Ashida, Ayaaki Kai, Kazuo Isobe, Tomoyasu Nishizawa, Shigeto Otsuka, Akira Yokota, Keishi Senoo, Satoshi Ishii
Nitrite reductase is a key enzyme for denitrification. There are two types of nitrite reductases: copper-containing NirK and cytochrome cd1 -containing NirS. Most denitrifiers possess either nirK or nirS, although a few strains been reported to possess both genes. We herein report the presence of nirK and nirS in the soil-denitrifying bacterium Bradyrhizobium sp. strain TSA1T . Both nirK and nirS were identified and actively transcribed under denitrification conditions. Based on physiological, chemotaxonomic, and genomic properties, strain TSA1T (=JCM 18858T =KCTC 62391T ) represents a novel species within the genus Bradyrhizobium, for which we propose the name Bradyrhizobium nitroreducens sp...
September 29, 2018: Microbes and Environments
Kamrun Naher, Hiroki Miwa, Shin Okazaki, Michiko Yasuda
Azospirillum sp. B510, a free-living nitrogen-fixing bacterium isolated from the stems of rice (Oryza sativa cv. Nipponbare), was investigated to establish effective conditions for the colonization of rice plants. We analyzed the effects of the nitrogen sources KNO3 , NH4 Cl, urea (CO[NH2 ]2 ), and NH4 NO3 at different concentrations (0.01-10 mM) on this colonization. Nitrogen promoted plant growth in a concentration-dependent manner, with minor differences being observed among the different nitrogen sources...
September 29, 2018: Microbes and Environments
Makoto Ikenaga, Shohei Katsuragi, Yoshihiro Handa, Hiroshi Katsumata, Naoya Chishaki, Tomohiro Kawauchi, Masao Sakai
PCR clamping by locked nucleic acid (LNA) oligonucleotides is an effective technique for selectively amplifying the community SSU rRNA genes of plant-associated bacteria. However, the original primer set often shows low amplification efficiency. In order to improve this efficiency, new primers were designed at positions to compete with LNA oligonucleotides. Three new sets displayed higher amplification efficiencies than the original; however, efficiency varied among the primer sets. Two new sets appeared to be available in consideration of bacterial profiles by next-generation sequencing...
September 29, 2018: Microbes and Environments
Amin Mojiri, Kazuma Nishimoto, Takanori Awata, Yoshiteru Aoi, Noriatsu Ozaki, Akiyoshi Ohashi, Tomonori Kindaichi
Four salts, SEALIFE (a synthetic sea salt), NaCl, Na2 SO4 , and NaCl+KCl, were applied to monitor the effects of salinity on "Candidatus Scalindua sp.", a marine anaerobic ammonium oxidation (anammox) bacterium. The highest ammonium consumption of 10 μmol mg protein-1 d-1 was observed at 88 mmol L-1 of Na in the presence of NaCl. The highest inorganic carbon uptake of 0.6 μmol mg protein-1 d-1 was observed at 117 mmol L-1 of Na and at 16 mmol L-1 of K in the presence of NaCl+KCl. Thus, Na and K are both important for maintaining a high growth rate of "Candidatus Scalindua sp...
September 29, 2018: Microbes and Environments
Yaping Wang, Tiantian Shi, Guoqiang Huang, Jun Gong
The present study aimed to reveal the eukaryotic diets of two economically important marine sediment-inhabiting worms, Sipunculus nudus (peanut worm) and Urechis unicinctus (spoon worm), using clone libraries and phylogenetic analyses of 18S rRNA genes. Fungal rDNA was also targeted and analyzed to reveal mycobiomes. Overall, we detected a wide range of eukaryotic phylotypes associated with the larvae of S. nudus and in the gut contents of both worms. These phylotypes included ciliates, diatoms, dinoflagellates, eustigmatophytes, placidids, oomycetes, fungi, nematodes, flatworms, seaweeds, and higher plants...
September 29, 2018: Microbes and Environments
Baodong Chen, Keiichiro Nayuki, Yukari Kuga, Xin Zhang, Songlin Wu, Ryo Ohtomo
Arbuscular mycorrhizal (AM) fungi can improve plant tolerance to heavy metal contamination. This detoxification ability may largely depend on how AM fungi influence the uptake and distribution of metals in host plants. Two experiments were performed in order to gain insights into the mechanisms underlying cadmium (Cd) tolerance in mycorrhizal plants. Stable isotope Cd106 and compartmented pots were adopted to quantify the contribution of the AM fungus, Rhizophagus irregularis, to the uptake of Cd by Lotus japonicus...
September 29, 2018: Microbes and Environments
Chiharu Iinuma, Akihiro Saito, Takayuki Ohnuma, Elodie Tenconi, Adeline Rosu, Séverine Colson, Yuuki Mizutani, Feng Liu, Magdalena Świątek-Połatyńska, Gilles P van Wezel, Sébastien Rigali, Takeshi Fujii, Kiyotaka Miyashita
In the model species Streptomyces coelicolor A3(2), the uptake of chitin-degradation byproducts, mainly N,N'- diacetylchitobiose ([GlcNAc]2 ) and N-acetylglucosamine (GlcNAc), is performed by the ATP-binding cassette (ABC) transporter DasABC-MsiK and the sugar-phosphotransferase system (PTS), respectively. Studies on the S. coelicolor chromosome have suggested the occurrence of additional uptake systems of GlcNAc-related compounds, including the SCO6005-7 cluster, which is orthologous to the ABC transporter NgcEFG of S...
September 29, 2018: Microbes and Environments
Pokchat Chutivisut, Kazuo Isobe, Sorawit Powtongsook, Wiboonluk Pungrasmi, Futoshi Kurisu
A dissimilatory nitrate reduction to ammonium (DNRA) microbial community was developed under a high organic carbon to nitrate (C/NO3 - ) ratio in an anoxic semi-continuous sequencing batch reactor (SBR) fed with glucose as the source of carbon and NO3 - as the electron acceptor. Activated sludge collected from a municipal wastewater treatment plant with good denitrification efficiency was used as the inoculum to start the system. The aim of this study was to examine the microbial populations in a high C/NO3 - ecosystem for potential DNRA microorganisms, which are the microbial group with the ability to reduce NO3 - to ammonium (NH4 + )...
September 29, 2018: Microbes and Environments
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