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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 13, 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 12, 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 8, 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 6, 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...
August 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...
August 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...
August 28, 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...
August 24, 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...
August 24, 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...
August 24, 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...
August 18, 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 + )...
August 9, 2018: Microbes and Environments
Chiharu Iinuma, Akihiro Saito, Takayuki Ohnuma, Elodie Tenconi, Adeline Rosu, Séverine Colson, Yuuki Mizutani, Feng Liu, Magdalena Świątek-Połatyńska, Gilles 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...
August 7, 2018: Microbes and Environments
Hui Zhu, Dong Zeng, Qiang Wang, Ning Wang, Bo Zeng, Lili Niu, Xueqin Ni
Diarrhea is often associated with marked alterations in the intestinal microbiota, termed dysbiosis; however, limited information is currently available on the intestinal microbiota in captive golden snub-nosed monkeys (Rhinopithecus roxellana) with diarrhea. We herein characterized the fecal microbiota in diarrhea and healthy monkeys using the Illumina MiSeq platform. The concentrations of fecal short-chain fatty acids (SCFAs) and copy numbers of virulence factor genes were also assessed using gas chromatography and quantitative PCR (qPCR), respectively...
July 25, 2018: Microbes and Environments
Yuki Morono, Tatsuhiko Hoshino, Takeshi Terada, Taketo Suzuki, Takahiro Sato, Hisashi Yuasa, Yuji Kubota, Fumio Inagaki
Experimental contamination by exogenous DNA is a major issue in molecular biological studies for data quality and its management. We herein assessed DNA aerosols for the risk of contamination and tested the capacity of clean air filters to trap and remove DNA aerosols. DNA aerosols were generated by atomizing a DNA solution and introduced into a laminar flow clean air unit. Capture and detection performed upstream and downstream of the clean air unit showed that a significant fraction (>99.96%) of introduced molecules was trapped and removed by the filter...
July 4, 2018: Microbes and Environments
Yingbo Duan, Biswarup Sen, Ningdong Xie, James S Paterson, Zixi Chen, Guangyi Wang
Marine fungus-like eukaryotic unicellular protists (thraustochytrids) are considered to play an important role in the marine microbial food web. However, their abundance, distribution, and relative biomass in coastal waters have not yet been examined in detail. By using a flow cytometry method (FCM) for the rapid enumeration of thraustochytrids in nearshore and offshore stations along the Gulf of Bohai, China, we herein expanded current knowledge on their ecological significance. The FCM method allows for the rapid detection and quantification of prokaryotic and eukaryotic cells, but is rarely applied to the enumeration of small eukaryotic protists...
July 4, 2018: Microbes and Environments
Daniel Sanhueza, Christine Chevillon, Nicolas Bouzinbi, Sylvain Godreuil, Jean-François Guégan
Species with a chitinous exoskeleton are overrepresented among the aquatic organisms carrying Mycobacterium ulcerans (MU) in nature and laboratory experiments have demonstrated the enhancing effects of chitin on the growth of MU. Field surveys identified pH as one of the key parameters delineating the distribution of MU in tropical regions. The present study investigated the relationship between chitin and pH in MU growth. By focusing on pH variations in the field, our results revealed that chitin enhanced MU growth in acidic environments...
July 4, 2018: Microbes and Environments
Makoto Matsushita, Kenta Magara, Yu Sato, Naoya Shinzato, Hiroyuki Kimura
Accretionary prisms are thick layers of sedimentary material piled up at convergent plate boundaries. Large amounts of anaerobic groundwater and methane (CH4 ) are contained in the deep aquifers associated with accretionary prisms. In order to identify microbial activity and CH4 production processes in the deep aquifers associated with the Cretaceous accretionary prism in Okinawa Island, Japan, we performed geochemical and microbiological studies using anaerobic groundwater and natural gas (mainly CH4 ) samples collected through four deep wells...
July 4, 2018: Microbes and Environments
Takafumi Kataoka, Satoshi Mitsunobu, Natsuko Hamamura
In the present study, the influence of the co-contamination with various chemical forms of antimony (Sb) with arsenite (As[III]) on soil microbial communities was investigated. The oxidation of As(III) to As(V) was monitored in soil columns amended with As(III) and three different chemical forms of Sb: antimony potassium tartrate (Sb[III]-tar), antimony(III) oxide (Sb2 O3 ), and potassium antimonate (Sb[V]). Soil microbial communities were examined qualitatively and quantitatively using 16S rDNA- and arsenite oxidase gene (aioA)-targeted analyses...
July 4, 2018: Microbes and Environments
Hye Young Ko, Kyuseon Cho, SungJun Park, Jin Hwi Kim, Joo-Hyon Kang, Yong Seok Jeong, Jong Duck Choi, Yongsik Sin, Cheonghoon Lee, GwangPyo Ko
Various waterborne pathogens originate from human or animal feces and may cause severe gastroenteric outbreaks. Bacteroides spp. that exhibit strong host- or group-specificities are promising markers for identifying fecal sources and their origins. In the present study, 240 water samples were collected from two major aquaculture areas in Republic of Korea over a period of approximately 1 year, and the concentrations and occurrences of four host-specific Bacteroides markers (human, poultry, pig, and ruminant) were evaluated in the study areas...
July 4, 2018: Microbes and Environments
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