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Microbes and Environments

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https://www.readbyqxmd.com/read/27885197/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#1
Nobutada Kimura, Yoichi Kamagata
A gene coding for a multicopper oxidase (BopA) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. The recombinant BopA protein produced in Escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in the presence of copper, suggesting that BopA is laccase. A bioinformatic analysis of the bopA gene sequence indicated that it has a phylogenetically bacterial origin, possibly derived from a bacterium within the phylum Deinococcus-Thermus...
November 23, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27867160/morphological-and-taxonomic-properties-of-tokyovirus-the-first-marseilleviridae-member-isolated-from-japan
#2
Masaharu Takemura
Members of the Marseilleviridae family are large DNA viruses with icosahedral particle structures that infect Acanthamoeba cells. The first Marseillevirus to be discovered was isolated in 2009. Since then, several other members of the Marseilleviridae family have been reported, including Lausannevirus, Senegalvirus, Cannes 8 virus, Insectomime virus, Tunisvirus, Melbournevirus, Port-Miou virus, and Brazilian Marseillevirus, which have been isolated from Europe, Africa, Australia, and South America. The morphological and genomic properties of a new Marseilleviridae family member, Tokyovirus, discovered in a water/soil sample from a Japanese river in Tokyo, were described in the present study...
November 19, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27867159/culture-dependent-and-independent-identification-of-polyphosphate-accumulating-dechloromonas-spp-predominating-in-a-full-scale-oxidation-ditch-wastewater-treatment-plant
#3
Mia Terashima, Ayano Yama, Megumi Sato, Isao Yumoto, Yoichi Kamagata, Souichiro Kato
The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp...
November 19, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27853060/physical-chemical-and-proteomic-evidence-of-potato-suberin-degradation-by-the-plant-pathogenic-bacterium-streptomyces-scabiei
#4
Carole Beaulieu, Amadou Sidibé, Raoudha Jabloune, Anne-Marie Simao-Beaunoir, Sylvain Lerat, Ernest Monga, Mark A Bernards
Potato peels consist of a tissue called phellem, which is formed by suberized cell layers. The degradation of suberin, a lipidic and recalcitrant polymer, is an ecological process attributed to soil fungal populations; however, previous studies have suggested that Streptomyces scabiei, the causal agent of potato common scab, possesses the ability to degrade suberin. In the present study, S. scabiei was grown in medium containing suberin-enriched potato phellem as the sole carbon source and its secretome was analyzed periodically (10- to 60-d-old cultures) with a special focus on proteins potentially involved in cell wall degradation...
November 17, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27795492/proteome-analyses-of-soil-bacteria-grown-in-the-presence-of-potato-suberin-a-recalcitrant-biopolymer
#5
Amadou Sidibé, Anne-Marie Simao-Beaunoir, Sylvain Lerat, Lauriane Giroux, Vicky Toussaint, Carole Beaulieu
Suberin is a complex lipidic plant polymer found in various tissues including the potato periderm. The biological degradation of suberin is attributed to fungi. Soil samples from a potato field were used to inoculate a culture medium containing suberin as the carbon source, and a metaproteomic approach was used to identify bacteria that developed in the presence of suberin over a 60-d incubation period. The normalized spectral counts of predicted extracellular proteins produced by the soil bacterial community markedly decreased from day 5 to day 20 and then slowly increased, revealing a succession of bacteria...
October 28, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27773914/diet-dependent-modular-dynamic-interactions-of-the-equine-cecal-microbiota
#6
Camilla Kristoffersen, Rasmus B Jensen, Ekaterina Avershina, Dag Austbø, Anne-Helene Tauson, Knut Rudi
Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg(-1) body weight per day) and a fiber-rich diet of only hay...
October 21, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27725345/bacterial-community-structures-in-freshwater-polar-environments-of-svalbard
#7
Spyridon Ntougias, Żaneta Polkowska, Sofia Nikolaki, Eva Dionyssopoulou, Panagiota Stathopoulou, Vangelis Doudoumis, Marek Ruman, Katarzyna Kozak, Jacek Namieśnik, George Tsiamis
Two thirds of Svalbard archipelago islands in the High Arctic are permanently covered with glacial ice and snow. Polar bacterial communities in the southern part of Svalbard were characterized using an amplicon sequencing approach. A total of 52,928 pyrosequencing reads were analyzed in order to reveal bacterial community structures in stream and lake surface water samples from the Fuglebekken and Revvatnet basins of southern Svalbard. Depending on the samples examined, bacterial communities at a higher taxonomic level mainly consisted either of Bacteroidetes, Betaproteobacteria, and Microgenomates (OP11) or Planctomycetes, Betaproteobacteria, and Bacteroidetes members, whereas a population of Microgenomates was prominent in 2 samples...
September 30, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27682804/in-situ-cultivation-allows-for-recovery-of-bacterial-types-competitive-in-their-natural-environment
#8
Dawoon Jung, Yoshiteru Aoi, Slava S Epstein
Standard cultivation fails to grow most microorganisms, whereas in situ cultivation allows for the isolation of comparatively diverse and novel microorganisms. Information on similarities and differences in the physiological properties of isolates obtained from in situ cultivation and standard cultivation is limited. Therefore, we used the arctic sediment samples and compared two culture collections obtained using standard and novel cultivation techniques. Even though there was no temperature selection at the isolation step, isolates from each method showed different reactions to temperature...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27682803/phylogenetic-identification-phenotypic-variations-and-symbiotic-characteristics-of-the-peculiar-rhizobium-strain-czr2-isolated-from-crotalaria-zanzibarica-in-taiwan
#9
Cheng-Tai Huang, Chi-Te Liu, Shiang-Jiuun Chen, Wen-Yuan Kao
Crotalaria zanzibarica is an exotic and widely distributed leguminous plant in Taiwan. The relationship between C. zanzibarica and its rhizobial symbionts has been suggested to contribute to its successful invasion. A rhizobial strain (designed as CzR2) isolated from the root nodules of C. zanzibarica and cultivated in standard YEM medium displayed pleomorphism, with cells ranging between 2 and 10 μm in length and some branching. In the present study, we identified this rhizobial strain, investigated the causes of pleomorphism, and examined the nodules formed...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27667143/complete-genome-sequencing-and-comparative-genomic-analysis-of-the-thermotolerant-acetic-acid-bacterium-acetobacter-pasteurianus-sku1108-provide-a-new-insight-into-thermotolerance
#10
Minenosuke Matsutani, Hideki Hirakawa, Eri Hiraoka, Gunjana Theeragool, Toshiharu Yakushi, Kazunobu Matsushita
Acetobacter pasteurianus SKU1108 is a typical thermotolerant acetic acid bacterium. In this study, the complete genome sequence of the SKU1108 strain was elucidated, and information on genomic modifications due to the thermal adaptation of SKU1108 was updated. In order to obtain a clearer understanding of the genetic background responsible for thermotolerance, the SKU1108 genome was compared with those of two closely related complete genome strains, thermotolerant A. pasteurianus 386B and mesophilic A. pasteurianus NBRC 3283...
September 24, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27645100/diversity-of-methane-oxidizing-bacteria-in-soils-from-hot-lands-of-medolla-italy-featured-by-anomalous-high-temperatures-and-biogenic-co2-emission
#11
Martina Cappelletti, Daniele Ghezzi, Davide Zannoni, Bruno Capaccioni, Stefano Fedi
"Terre Calde di Medolla" (TCM) (literally, "Hot Lands of Medolla") refers to a farming area in Italy with anomalously high temperatures and diffuse emissions of biogenic CO2, which has been linked to CH4 oxidation processes from a depth of 0.7 m to the surface. We herein assessed the composition of the total bacterial community and diversity of methane-oxidizing bacteria (MOB) in soil samples collected at a depth at which the peak temperature was detected (0.6 m). Cultivation-independent methods were used, such as: i) a clone library analysis of the 16S rRNA gene and pmoA (coding for the α-subunit of the particulate methane monooxygenase) gene, and ii) Terminal Restriction Fragment Length Polymorphism (T-RFLP) fingerprinting...
September 17, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27629106/iron-availability-modulates-the-persistence-of-legionella-pneumophila-in-complex-biofilms
#12
Emilie Portier, Joanne Bertaux, Jérôme Labanowski, Yann Hechard
Legionella pneumophila is a pathogenic bacteria found in biofilms in freshwater. Iron is an essential nutrient for L. pneumophila growth. In this study, complex biofilms were developed using river water spiked with L. pneumophila, and the persistence of L. pneumophila in these complex biofilms was evaluated. In order to study the role of iron in the persistence of L. pneumophila, river water was supplied with either iron pyrophosphate or iron chelators (deferoxamine mesylate, DFX for ferric iron and dipyridyl, DIP for ferrous iron) to modulate iron availability...
September 14, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27600711/application-of-locked-nucleic-acid-lna-primer-and-pcr-clamping-by-lna-oligonucleotide-to-enhance-the-amplification-of-internal-transcribed-spacer-its-regions-in-investigating-the-community-structures-of-plant-associated-fungi
#13
Makoto Ikenaga, Masakazu Tabuchi, Tomohiro Kawauchi, Masao Sakai
The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant-associated fungi due to the similar homologies of sequences in primer-annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27600710/effect-of-elevated-co2-concentration-elevated-temperature-and-no-nitrogen-fertilization-on-methanogenic-archaeal-and-methane-oxidizing-bacterial-community-structures-in-paddy-soil
#14
Dongyan Liu, Kanako Tago, Masahito Hayatsu, Takeshi Tokida, Hidemitsu Sakai, Hirofumi Nakamura, Yasuhiro Usui, Toshihiro Hasegawa, Susumu Asakawa
Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27592518/regional-variation-of-ch4-and-n2-production-processes-in-the-deep-aquifers-of-an-accretionary-prism
#15
Makoto Matsushita, Shugo Ishikawa, Kazushige Nagai, Yuichiro Hirata, Kunio Ozawa, Satoshi Mitsunobu, Hiroyuki Kimura
Accretionary prisms are mainly composed of ancient marine sediment scraped from the subducting oceanic plate at a convergent plate boundary. Large amounts of anaerobic groundwater and natural gas, mainly methane (CH4) and nitrogen gas (N2), are present in the deep aquifers associated with an accretionary prism; however, the origins of these gases are poorly understood. We herein revealed regional variations in CH4 and N2 production processes in deep aquifers in the accretionary prism in Southwest Japan, known as the Shimanto Belt...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27558588/an-evaluation-method-for-the-suppression-of-pathogenic-fusarium-oxysporum-by-soil-microorganisms-using-the-dilution-plate-technique
#16
Masahiro Mitsuboshi, Yuuzou Kioka, Katsunori Noguchi, Susumu Asakawa
Soil-borne diseases caused by pathogenic microorganisms are one of the main factors responsible for the decline in crop yields in farmlands. Pathogenic Fusarium oxysporum causes serious damage to various crops, and, thus, a feasible diagnostic method for soil-borne diseases is required. We herein examined a simple method to evaluate the suppressiveness of soil microorganisms against a pathogen by co-cultivating indigenous soil microorganisms and a pathogenic fungus (F. oxysporum f. sp. spinaciae). We inoculated F...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27524305/bacterial-communities-associated-with-different-anthurium-andraeanum-l-plant-tissues
#17
Yohanna Sarria-Guzmán, Yosef Chávez-Romero, Selene Gómez-Acata, Joaquín Adolfo Montes-Molina, Eleacin Morales-Salazar, Luc Dendooven, Yendi E Navarro-Noya
Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27524304/composition-of-the-cockroach-gut-microbiome-in-the-presence-of-parasitic-nematodes
#18
Cláudia S L Vicente, Sota Ozawa, Koichi Hasegawa
Cockroaches are parasitized by thelastomatid nematodes, which live in an obligate manner in their hindgut and interact with the resident microbial community. In the present study, a composition analysis was performed on the gut microbiome of Periplaneta fuliginosa and P. americana to investigate natural and artificial infection by thelastomatid nematodes. Nine libraries of the 16S rRNA gene V3-V4 region were prepared for pyrosequencing. We examined the complete gut microbiome (fore-, mid-, and hindgut) of lab-reared P...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27453124/phylogenetically-diverse-aerobic-anoxygenic-phototrophic-bacteria-isolated-from-epilithic-biofilms-in-tama-river-japan
#19
Setsuko Hirose, Katsumi Matsuura, Shin Haruta
The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27431485/comparative-genomics-of-syntrophic-branched-chain-fatty-acid-degrading-bacteria
#20
Takashi Narihiro, Masaru K Nobu, Hideyuki Tamaki, Yoichi Kamagata, Yuji Sekiguchi, Wen-Tso Liu
The syntrophic degradation of branched-chain fatty acids (BCFAs) such as 2-methylbutyrate and isobutyrate is an essential step in the production of methane from proteins/amino acids in anaerobic ecosystems. While a few syntrophic BCFA-degrading bacteria have been isolated, their metabolic pathways in BCFA and short-chain fatty acid (SCFA) degradation as well as energy conservation systems remain unclear. In an attempt to identify these pathways, we herein performed comparative genomics of three syntrophic bacteria: 2-methylbutyrate-degrading "Syntrophomonas wolfei subsp...
September 29, 2016: Microbes and Environments
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