Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences.

abstract：:To assess the role of open-ocean ecosystems in global CO2 fixation, we investigated how picophytoplankton, which dominate primary production, responded to episodic increases in nutrient availability. Previous experiments have shown nitrogen alone, or in combination with phosphorus or iron, to be the proximate limiting...

journal_title：Environmental microbiology reports

authors： Grob C,Jardillier L,Hartmann M,Ostrowski M,Zubkov MV,Scanlan DJ

更新日期：2015-04-01 00:00:00

abstract：:We undertook a large-scale epidemiological survey of commensal Escherichia coli in Trois-Sauts, an isolated village located in the south of French Guiana where human population exchanges are restricted and source of antibiotics controlled. Stools from 162 Wayampi Amerindians and rectal swabs from 33 human associated a...

journal_title：Environmental microbiology reports

authors： Lescat M,Clermont O,Woerther PL,Glodt J,Dion S,Skurnik D,Djossou F,Dupont C,Perroz G,Picard B,Catzeflis F,Andremont A,Denamur E

更新日期：2013-02-01 00:00:00

abstract：:The increase in the areal extent of the subtropical gyres over the past decade has been attributed to a global tendency towards increased water-column stratification. Here, we examine how vertical stratification governs the community structure of the picophytoplankton that dominate these vast marine ecosystems. We ana...

journal_title：Environmental microbiology reports

authors： Bouman HA,Ulloa O,Barlow R,Li WK,Platt T,Zwirglmaier K,Scanlan DJ,Sathyendranath S

更新日期：2011-08-01 00:00:00

abstract：:KaiC protein is the pivotal component of the circadian clock in cyanobacteria. While KaiC family proteins are well-conserved throughout divergent phylogenetic lineages, studies of the physiological roles of KaiC proteins from other microorganisms have been limited. We examined the role of the KaiC proteins, KaiC1 and ...

journal_title：Environmental microbiology reports

authors： Iguchi H,Yoshida Y,Fujisawa K,Taga H,Yurimoto H,Oyama T,Sakai Y

更新日期：2018-12-01 00:00:00

abstract：:The cyanobacterial species Planktothrix rubescens is known to preferably inhabit deep, stratified, oligo- to mesotrophic lakes. It is also known for the production of diverse bioactive peptides, including the hepatotoxic microcystins. A number of studies showed that P. rubescens populations generally consist of multip...

journal_title：Environmental microbiology reports

authors： Haruštiaková D,Welker M

更新日期：2017-04-01 00:00:00

abstract：:Tropospheric nitrate levels are predicted to increase throughout the 21st century, with potential effects on terrestrial ecosystems, including the Greenland ice sheet (GrIS). This study considers the impacts of elevated nitrate concentrations on the abundance and composition of dominant bulk and active prokaryotic com...

journal_title：Environmental microbiology reports

authors： Cameron KA,Stibal M,Chrismas N,Box J,Jacobsen CS

更新日期：2017-04-01 00:00:00

abstract：:The Epsilonproteobacteria, including members of the genus Sulfurovum, are regarded as important primary producers in hydrothermal systems. However, their in situ gene expression in this habitat has so far not been investigated. We report a metatranscriptomic analysis of a Sulfurovum-dominated biofilm from one of the c...

journal_title：Environmental microbiology reports

authors： Dahle H,Roalkvam I,Thorseth IH,Pedersen RB,Steen IH

更新日期：2013-04-01 00:00:00

abstract：:Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin binding protein and a virulence factor involved in the colonization of human intestine. We investigated the distribution and genetic variations of gbpA in 488 V. cholerae strains of environmental and clinical origin, belonging to different serog...

journal_title：Environmental microbiology reports

authors： Stauder M,Huq A,Pezzati E,Grim CJ,Ramoino P,Pane L,Colwell RR,Pruzzo C,Vezzulli L

更新日期：2012-08-01 00:00:00

abstract：:Electrodes poised at potentials low enough to serve as an electron donor for microbial respiration, but high enough to avoid the production of hydrogen, have been proposed as an alternative to the use of soluble electron donors for stimulating the bioremediation of chlorinated contaminants and/or metals. However, this...

journal_title：Environmental microbiology reports

authors： Strycharz SM,Gannon SM,Boles AR,Franks AE,Nevin KP,Lovley DR

更新日期：2010-04-01 00:00:00

abstract：:The community composition of bacteria with highly dynamic abundance and activity was observed to be with low variability in a shallow lake sediment with frequent physical disturbance. This suggests that physical disturbance did not create more niches and did not lead to highly variable bacterial community. The major p...

journal_title：Environmental microbiology reports

authors： Tšertova N,Kisand A,Tammert H,Kisand V

更新日期：2011-04-01 00:00:00

abstract：:Antarctic terrestrial ecosystems are largely dominated by lichens, while shallow coastal environments are mainly covered by macroalgae. The aim of this study was to isolate and to evaluate the diversity of yeasts in different species of macroalgae and lichens collected in South Shetland Islands, Antarctica. A total of...

journal_title：Environmental microbiology reports

authors： Duarte AWF,Passarini MRZ,Delforno TP,Pellizzari FM,Cipro CVZ,Montone RC,Petry MV,Putzke J,Rosa LH,Sette LD

更新日期：2016-10-01 00:00:00

abstract：:Bacteria from the Chloroflexi phylum are dominant members of phototrophic microbial mat communities in terrestrial thermal environments. Vitamins of B group are key intermediates (precursors) in the biosynthesis of indispensable enzyme cofactors driving numerous metabolic processes in all forms of life. A genomics-bas...

journal_title：Environmental microbiology reports

authors： Rodionova IA,Li X,Plymale AE,Motamedchaboki K,Konopka AE,Romine MF,Fredrickson JK,Osterman AL,Rodionov DA

更新日期：2015-04-01 00:00:00

abstract：:The extent to which different sequence-based approaches describe environmental microbial communities in comparative studies is an important consideration when deriving inferences from ecological studies. The ability of a targeted metagenomic approach [small subunit (SSU) rRNA pyrosequencing] and shotgun metagenome app...

journal_title：Environmental microbiology reports

authors： Steven B,Gallegos-Graves LV,Starkenburg SR,Chain PS,Kuske CR

更新日期：2012-04-01 00:00:00

abstract：:Lack of the Pseudomonas putida PP2258 protein or its overexpression results in defective motility on solid media. The PP2258 protein is tripartite, possessing a PAS domain linked to two domains associated with turnover of c-di-GMP - a cyclic nucleotide that controls the switch between motile and sessile lifestyles. Th...

journal_title：Environmental microbiology reports

authors： Österberg S,Åberg A,Herrera Seitz MK,Wolf-Watz M,Shingler V

更新日期：2013-08-01 00:00:00

abstract：:Pseudomonas putida S12.49, a mutant stain of P. putida S12 that tolerates up to 20 mM benzene, was obtained by evolutionary selection. The genetic basis for the strongly enhanced benzene tolerance was investigated by proteome and transcriptome analysis. Indications were found that the highly benzene-tolerant phenotype...

journal_title：Environmental microbiology reports

authors： Volkers RJ,Ballerstedt H,De Winde JH,Ruijssenaars HJ

更新日期：2010-06-01 00:00:00

abstract：:Infection of honeybees by the microsporidian Nosema ceranae is considered to be one of the factors underlying the increased colony losses and decreased honey production seen in recent years. However, these effects appear to differ in function of the climatic zone, the distinct beekeeping practices and the honeybee spe...

journal_title：Environmental microbiology reports

authors： Van der Zee R,Gómez-Moracho T,Pisa L,Sagastume S,García-Palencia P,Maside X,Bartolomé C,Martín-Hernández R,Higes M

更新日期：2014-08-01 00:00:00

abstract：:Tunicates are useful models for exploring microbiomes because they have an innate immune system resembling that of chordates. Automated ribosomal RNA intergenic spacer analysis and High-Throughput Sequencing were used to compare the tunic microbiomes of Ciona robusta (formerly Ciona intestinalis type A), Ciona savigny...

journal_title：Environmental microbiology reports

authors： Cahill PL,Fidler AE,Hopkins GA,Wood SA

更新日期：2016-08-01 00:00:00

abstract：:Rice plants play a key role in regulating methane emissions from paddy fields by affecting both underlying processes: methane production and oxidation. Specific differences were reported for methane oxidation rates; however, studies on the bacterial communities involved are rare. Here, we analysed the methanotrophic c...

journal_title：Environmental microbiology reports

authors： Lüke C,Bodrossy L,Lupotto E,Frenzel P

更新日期：2011-10-01 00:00:00

abstract：:A fundamental question in marine microbial ecology is how microbes adapt to ocean environments. Although numerically dominant populations are typically considered more successful, higher census population sizes (Nc) do not equate directly to a greater capability for adaptation. Instead, effective population size (Ne) ...

journal_title：Environmental microbiology reports

authors： Luo H,Swan BK,Stepanauskas R,Hughes AL,Moran MA

更新日期：2014-04-01 00:00:00

abstract：:Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functio...

journal_title：Environmental microbiology reports

authors： Guan Y,Haroon MF,Alam I,Ferry JG,Stingl U

更新日期：2017-08-01 00:00:00

abstract：:Bacterial community compositions (BCC) associated with the cladoceran Bosmina coregoni and the cyclopoid copepod Thermocyclops oithonoides in oligotrophic Lake Stechlin versus eutrophic Lake Dagow (northeastern Germany) were compared using molecular techniques. We also transplanted the zooplankton from their native la...

journal_title：Environmental microbiology reports

authors： Grossart HP,Dziallas C,Tang KW

更新日期：2009-02-01 00:00:00

abstract：:This study examined total uptake of extracellular polymeric substances (EPS) and glucose and the percentage of prokaryotic cells (Bacteria, Crenarchaea and Euryarchaea) consuming these compounds in the major water masses at the DYFAMED site (NW Mediterranean Sea). The potential assimilation rates of EPS at 10 m depth ...

journal_title：Environmental microbiology reports

authors： Boutrif M,Garel M,Cottrell MT,Tamburini C

更新日期：2011-12-01 00:00:00

abstract：:Magnetotactic bacteria are capable of aligning and swimming along the geomagnetic field lines; such a behaviour is called magnetotaxis. Previous studies reported that bacteria in the northern hemisphere migrate preferentially towards the North Pole of the Earth's magnetic field (north-seeking, NS), whereas those in th...

journal_title：Environmental microbiology reports

authors： Zhang WJ,Chen C,Li Y,Song T,Wu LF

更新日期：2010-10-01 00:00:00

abstract：:Corals are inhabited by complex communities of microbes that affect their growth and survival. Several studies suggest that coral disease may be attributed to the success of vibrios in out-competing other bacteria in the mucus and tissues of corals. Vibrios utilize a variety of quorum sensing (QS) signal molecules to ...

journal_title：Environmental microbiology reports

authors： Tait K,Hutchison Z,Thompson FL,Munn CB

更新日期：2010-02-01 00:00:00

abstract：:Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co-cultivated with their hosts, and until now no nanoarchaeotal cultures or genomes have been described from deep-sea hydrothermal v...

journal_title：Environmental microbiology reports

authors： St John E,Flores GE,Meneghin J,Reysenbach AL

更新日期：2019-04-01 00:00:00

abstract：:Amphibians are in decline as a result of habitat destruction, climate change and infectious diseases. Tadpoles are thought susceptible to infections because they are dependent on only an innate immune system (e.g. macrophages). This is because the frog adaptive immune system does not function until later stages of the...

journal_title：Environmental microbiology reports

authors： Chambouvet A,Valigurová A,Pinheiro LM,Richards TA,Jirků M

更新日期：2016-10-01 00:00:00

abstract：:Aspergillus fumigatus and free-living amoebae are common inhabitants of soil. Mechanisms of A. fumigatus to circumvent the amoeba's digestion may facilitate overcoming the vertebrate macrophage defence mechanisms. We performed co-culture experiments using A. fumigatus conidia and the amoeba Acanthamoeba castellanii. A...

journal_title：Environmental microbiology reports

authors： Van Waeyenberghe L,Baré J,Pasmans F,Claeys M,Bert W,Haesebrouck F,Houf K,Martel A

更新日期：2013-12-01 00:00:00

abstract：:In the last few years, geomicrobiologists have focused their researches on the nature and origin of enigmatic reticulated filaments reported in modern and fossil samples from limestone caves and basalt lava tubes. Researchers have posed questions on these filaments concerning their nature, origin, chemistry, morpholog...

journal_title：Environmental microbiology reports

authors： Miller AZ,Hernández-Mariné M,Jurado V,Dionísio A,Barquinha P,Fortunato E,Afonso MJ,Chaminé HI,Saiz-Jimenez C

更新日期：2012-12-01 00:00:00

abstract：:Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-ind...

journal_title：Environmental microbiology reports

authors： McDermott TR,Stolz JF,Oremland RS

更新日期：2020-04-01 00:00:00

abstract：:Pseudomonas putida KF715 exhibits unique properties in both catabolic activity and genome plasticity. Our previous studies revealed that the DNA region containing biphenyl and salycilate metabolism gene clusters (termed the bph-sal element) was frequently deleted and transferred by conjugation to closely related P. pu...

journal_title：Environmental microbiology reports

authors： Suenaga H,Fujihara H,Kimura N,Hirose J,Watanabe T,Futagami T,Goto M,Shimodaira J,Furukawa K

更新日期：2017-10-01 00:00:00