Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

abstract：:To determine whether the distribution of estuarine ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteobacterial ammonia oxidizers (AOB) was characterized along a salinity gradient in sediments of the Ythan estuary, on the east coast of Scotland, UK, by denaturant gradient...

journal_title：Environmental microbiology

authors： Freitag TE,Chang L,Prosser JI

更新日期：2006-04-01 00:00:00

abstract：:The cosmopolitan coccolithophore Emiliania huxleyi is characterized by a strongly differentiated haplodiplontic life cycle consisting of a diploid phase, generally bearing coccoliths (calcified) but that can be also non-calcified, and a non-calcified biflagellated haploid phase. Given most studies have focused on the ...

journal_title：Environmental microbiology

authors： Frada MJ,Bidle KD,Probert I,de Vargas C

更新日期：2012-06-01 00:00:00

abstract：:In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea wate...

journal_title：Environmental microbiology

authors： Kasai Y,Kishira H,Syutsubo K,Harayama S

更新日期：2001-04-01 00:00:00

abstract：:Phosphonoacetate is regarded as an antiviral xenobiotic whose mineralization can be catalysed by an enzyme, phosphonoacetate hydrolase, encoded by the phnA gene. To date the enzyme's activity has been detected in only a limited number of bacteria. Its expression has been shown to occur in a manner independent of the p...

journal_title：Environmental microbiology

authors： Panas P,Ternan NG,Dooley JS,McMullan G

更新日期：2006-05-01 00:00:00

abstract：:The Pmk1 and Mps1 MAP kinases are essential for appressorium formation and plant infection in Magnaporthe oryzae. However, their exact roles during invasive growth are not clear because pmk1 and mps1 mutants are defective in penetration. To further characterize their functions after penetration, in this study we expre...

journal_title：Environmental microbiology

authors： Zhang X,Liu W,Li Y,Li G,Xu JR

更新日期：2017-10-01 00:00:00

abstract：:The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typi...

journal_title：Environmental microbiology

authors： Kim E,Sprung B,Duhamel S,Filardi C,Kyoon Shin M

更新日期：2016-12-01 00:00:00

abstract：:The structure of bacterial communities in first-year spring and summer sea ice differs from that in source seawaters, suggesting selection during ice formation in autumn or taxon-specific mortality in the ice during winter. We tested these hypotheses by weekly sampling (January-March 2004) of first-year winter sea ice...

journal_title：Environmental microbiology

authors： Collins RE,Rocap G,Deming JW

更新日期：2010-07-01 00:00:00

abstract：:Pathogenic bacteria associated with freshwater ecosystems can pose significant health risks particularly where recreational water use is popular. Common water quality assessments involve quantifying indicator Escherichia coli within the water column but neglect to consider physical and geochemical factors and contribu...

journal_title：Environmental microbiology

authors： VanMensel D,Chaganti SR,Droppo IG,Weisener CG

更新日期：2020-02-01 00:00:00

abstract：:Acid rain can cause severe effects on soil biota and nutrient biogeochemical cycles in the forest ecosystem, but how plant-symbiotic ectomycorrhizal fungi will modulate the effects remains unknown. Here, we conducted a full factorial field experiment in a Masson pine forest by simultaneously controlling the acidity of...

journal_title：Environmental microbiology

authors： Li Y,Chen Z,He JZ,Wang Q,Shen C,Ge Y

更新日期：2019-01-01 00:00:00

abstract：:Bacteriophages, the viruses that infect bacteria, are the most abundant biological entities in the biosphere and play a key role in global biogeochemical cycling. All T4-type bacteriophage isolates tested so far have a conserved genetic module that encodes the virion components including gene 23 (g23), the major capsi...

journal_title：Environmental microbiology

authors： Jia Z,Ishihara R,Nakajima Y,Asakawa S,Kimura M

更新日期：2007-04-01 00:00:00

abstract：:Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on...

journal_title：Environmental microbiology

authors： Scheublin TR,Deusch S,Moreno-Forero SK,Müller JA,van der Meer JR,Leveau JH

更新日期：2014-07-01 00:00:00

abstract：:Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remai...

journal_title：Environmental microbiology

authors： Xie W,Luo H,Murugapiran SK,Dodsworth JA,Chen S,Sun Y,Hedlund BP,Wang P,Fang H,Deng M,Zhang CL

更新日期：2018-02-01 00:00:00

abstract：:Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylo...

journal_title：Environmental microbiology

authors： Nicol GW,Leininger S,Schleper C,Prosser JI

更新日期：2008-11-01 00:00:00

abstract：:Marine myoviruses (i.e. bacteriophages with a contractile tail sheath) are numerically abundant and genetically diverse. We developed a terminal restriction fragment length polymorphism assay (TRFLP) for g23, the conserved gene encoding the major capsid protein, to investigate T4-like myovirus communities at USC's Mic...

journal_title：Environmental microbiology

authors： Chow CE,Fuhrman JA

更新日期：2012-08-01 00:00:00

abstract：:Major concern in the Mixed Crop-Livestock (MCL) farms, in which livestock and vegetables grown closely in the same facility, is cross-contamination of zoonotic bacterial pathogens especially Salmonella. To investigate the distribution of Salmonella serovars in MCL and their products, a total of 1287 pre-harvest sample...

journal_title：Environmental microbiology

authors： Peng M,Salaheen S,Almario JA,Tesfaye B,Buchanan R,Biswas D

更新日期：2016-05-01 00:00:00

abstract：:Bacterial and archaeal assemblages have been studied in a multipond solar saltern using a range of microbial ecology techniques by four laboratories simultaneously. These include 16S rDNA sequencing from both denaturing gradient gel electrophoresis (DGGE) and clone libraries, and culturing methods. Water samples from ...

journal_title：Environmental microbiology

authors： Benlloch S,López-López A,Casamayor EO,Øvreås L,Goddard V,Daae FL,Smerdon G,Massana R,Joint I,Thingstad F,Pedrós-Alió C,Rodríguez-Valera F

更新日期：2002-06-01 00:00:00

abstract：:Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of the ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled the ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large se...

journal_title：Environmental microbiology

authors： Duarte CM,Ngugi DK,Alam I,Pearman J,Kamau A,Eguiluz VM,Gojobori T,Acinas SG,Gasol JM,Bajic V,Irigoien X

更新日期：2020-11-01 00:00:00

abstract：:Growing evidence indicates that dense water formation and flow over the continental shelf is a globally relevant oceanographic process, potentially affecting microbial assemblages down to the deep ocean. However, the extent and consequences of this influence have yet to be investigated. Here it is shown that dense wat...

journal_title：Environmental microbiology

authors： Luna GM,Chiggiato J,Quero GM,Schroeder K,Bongiorni L,Kalenitchenko D,Galand PE

更新日期：2016-12-01 00:00:00

abstract：:Selection of suitable genotypes from diverse seed banks may help phytoplankton populations to cope with environmental changes. This study examines whether the high genotypic diversity found in the Baltic cyst pool of the toxic dinoflagellate Alexandrium ostenfeldii is coupled to phenotypic variability that could aid s...

journal_title：Environmental microbiology

authors： Kremp A,Oja J,LeTortorec AH,Hakanen P,Tahvanainen P,Tuimala J,Suikkanen S

更新日期：2016-02-01 00:00:00

abstract：:Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communi...

journal_title：Environmental microbiology

authors： Briggs BR,Brodie EL,Tom LM,Dong H,Jiang H,Huang Q,Wang S,Hou W,Wu G,Huang L,Hedlund BP,Zhang C,Dijkstra P,Hungate BA

更新日期：2014-06-01 00:00:00

abstract：:Bacterial degradation of polycyclic aromatic hydrocarbons (PAHs), ubiquitous contaminants from oil and coal, is typically limited by poor accessibility of the contaminant to the bacteria. In order to measure PAH availability in complex systems, we designed a number of diffusion-based assays with a double-tagged bacter...

journal_title：Environmental microbiology

authors： Tecon R,Binggeli O,van der Meer JR

更新日期：2009-09-01 00:00:00

abstract：:The marine gamma-Proteobacterium Alcanivorax borkumensis is highly specialized in the assimilation of aliphatic hydrocarbons, and makes up a large part of the biomass in oil-polluted marine environments. In addition to the previously identified alkane hydroxylase AlkB1, a second alkane hydroxylase (AlkB2) showing 65% ...

journal_title：Environmental microbiology

authors： van Beilen JB,Marín MM,Smits TH,Röthlisberger M,Franchini AG,Witholt B,Rojo F

更新日期：2004-03-01 00:00:00

abstract：:Autophagy is a conserved degradation system in eukaryotic cells that includes non-selective and selective processes. Selective autophagy functions as a selective degradation mechanism for specific substrates in which autophagy-related protein 11 (ATG11) acts as an essential scaffold protein. In B. bassiana, there is a...

journal_title：Environmental microbiology

authors： Ding JL,Peng YJ,Chu XL,Feng MG,Ying SH

更新日期：2018-09-01 00:00:00

abstract：:Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation-dependent and independent approaches to analyse...

journal_title：Environmental microbiology

authors： Miranda-Sánchez F,Rivera J,Vinuesa P

更新日期：2016-09-01 00:00:00

abstract：:Autotrophic carbon dioxide (CO2 ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metag...

journal_title：Environmental microbiology

authors： Xiao KQ,Ge TD,Wu XH,Peacock CL,Zhu ZK,Peng J,Bao P,Wu JS,Zhu YG

更新日期：2020-08-21 00:00:00

abstract：:Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide preci...

journal_title：Environmental microbiology

authors： Glass JB,Yu H,Steele JA,Dawson KS,Sun S,Chourey K,Pan C,Hettich RL,Orphan VJ

更新日期：2014-06-01 00:00:00

abstract：:Biological membranes have evolved different mechanisms to modify their composition in response to chemical stimuli in a process called 'homeoviscous adaptation'. Among these mechanisms, modifications in the ratio of saturated/unsaturated fatty acids and in cis/trans fatty acid isomers, cyclopropanation and changes in ...

journal_title：Environmental microbiology

authors： Bernal P,Muñoz-Rojas J,Hurtado A,Ramos JL,Segura A

更新日期：2007-05-01 00:00:00

abstract：:Petrochemical and geological evidence suggest that petroleum in most reservoirs is anaerobically biodegraded to some extent. However, the conditions for this metabolism and the cultivation of the requisite microorganisms are rarely established. Here, we report on microbial hydrocarbon metabolism in two distinct oilfie...

journal_title：Environmental microbiology

authors： Gieg LM,Davidova IA,Duncan KE,Suflita JM

更新日期：2010-11-01 00:00:00

abstract：:Tropical aquatic legumes of the genus Aeschynomene are unique in that they can be stem-nodulated by photosynthetic bradyrhizobia. Moreover, a recent study demonstrated that two Aeschynomene indica symbionts lack canonical nod genes, thereby raising questions about the distribution of such atypical symbioses among rhiz...

journal_title：Environmental microbiology

authors： Miché L,Moulin L,Chaintreuil C,Contreras-Jimenez JL,Munive-Hernández JA,Del Carmen Villegas-Hernandez M,Crozier F,Béna G

更新日期：2010-08-01 00:00:00

abstract：:The distribution and the metabolic pathways of bacteria degrading steroid compounds released by eukaryotic organisms were investigated using the bile salt cholate as model substrate. Cholate-degrading bacteria could be readily isolated from freshwater environments. All isolated strains transiently released steroid deg...

journal_title：Environmental microbiology

authors： Holert J,Yücel O,Suvekbala V,Kulić Z,Möller H,Philipp B

更新日期：2014-05-01 00:00:00