Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries.

abstract：:Nostoc flagelliforme is well known for its strong ecological adaptability in inhabiting desert biological soil crusts. However, the mechanism of its recovery from quiescent to active state after prolonged dormancy remains poorly characterized. Especially how exoproteome be related to the adaptive strategies and partic...

journal_title：Environmental microbiology

authors： Wang B,Yang J,Xu C,Yi L,Wan C

更新日期：2020-04-01 00:00:00

abstract：:We have surveyed the first 1 m of 10 oligotrophic high mountain lakes in the Central Pyrenees (Spain) for both abundance and predominant phylotypes richness of the archaeaplankton assemblage, using CARD-FISH and 16S rRNA gene sequencing respectively. Archaea inhabiting the air-water surface microlayer (neuston) ranged...

journal_title：Environmental microbiology

authors： Auguet JC,Casamayor EO

更新日期：2008-04-01 00:00:00

abstract：:Arctic marine microbes are affected by environmental changes that may ultimately influence their functions in carbon cycling. Here, we investigated in concert the structure and enzymatic activities of pelagic, particle-associated and benthic bacterial communities in the central Arctic Ocean, and used these data to eva...

journal_title：Environmental microbiology

authors： Balmonte JP,Teske A,Arnosti C

更新日期：2018-08-01 00:00:00

abstract：:Chemolithoautotrophic nitrite oxidizers of the genus Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natural habitats, and play a key role in nitrogen elimination during biological wastewater treatment. Phylogenetic analyses of cloned 16S rRNA genes and fluorescence in situ...

journal_title：Environmental microbiology

authors： Maixner F,Noguera DR,Anneser B,Stoecker K,Wegl G,Wagner M,Daims H

更新日期：2006-08-01 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：:Photosynthetic microorganisms play a crucial role in the marine environment. In vast areas of the oceans, marine primary productivity is performed by cells smaller than 2-3 micro m (picoplankton). Here, we report on molecular analyses of the conserved photosynthetic psbA gene (coding for protein D1 of photosystem II r...

journal_title：Environmental microbiology

authors： Zeidner G,Preston CM,Delong EF,Massana R,Post AF,Scanlan DJ,Béjà O

更新日期：2003-03-01 00:00:00

abstract：:The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the ...

journal_title：Environmental microbiology

authors： Taubert M,Grob C,Crombie A,Howat AM,Burns OJ,Weber M,Lott C,Kaster AK,Vollmers J,Jehmlich N,von Bergen M,Chen Y,Murrell JC

更新日期：2019-10-01 00:00:00

abstract：:Chloride channel proteins (ClC) are found in living systems where they transport chloride ions across cell membranes. Recently, the structure/function of two prokaryotic ClC has been determined but little is known about the role of these proteins in the microbial metabolism of chlorinated compounds. Here we show that ...

journal_title：Environmental microbiology

authors： Sebastianelli A,Bruce IJ

更新日期：2007-01-01 00:00:00

abstract：:Symbiotic associations between microbes and invertebrates have resulted in some of the most unusual physiological and morphological adaptations that have evolved in the animal world. We document a new symbiosis between marine polychaetes of the genus Osedax and members of the bacterial group Oceanospirillales, known f...

journal_title：Environmental microbiology

authors： Goffredi SK,Orphan VJ,Rouse GW,Jahnke L,Embaye T,Turk K,Lee R,Vrijenhoek RC

更新日期：2005-09-01 00:00:00

abstract：:Model denitrifiers convert NO3- to N2 , but it appears that a significant fraction of natural populations are truncated, conducting only one or two steps of the pathway. To better understand the diversity of partial denitrifiers in soil and whether discrepancies arise between the presence of known N-oxide reductase ge...

journal_title：Environmental microbiology

authors： Roco CA,Bergaust LL,Bakken LR,Yavitt JB,Shapleigh JP

更新日期：2017-06-01 00:00:00

abstract：:Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22 Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X...

journal_title：Environmental microbiology

authors： Leong SL,Lantz H,Pettersson OV,Frisvad JC,Thrane U,Heipieper HJ,Dijksterhuis J,Grabherr M,Pettersson M,Tellgren-Roth C,Schnürer J

更新日期：2015-02-01 00:00:00

abstract：:Contaminated soils are subject to diurnal and seasonal temperature variations during on-site ex-situ bioremediation processes. We assessed how diurnal temperature variations similar to that in summer at the site from which petroleum hydrocarbon-contaminated soil was collected affect the soil microbial community and th...

journal_title：Environmental microbiology

authors： Akbari A,Ghoshal S

更新日期：2015-12-01 00:00:00

abstract：:The presence of two insertion sequences, IS406 and IS407, was tested by polymerase chain reaction (PCR) amplification in 25 strains representing 15 Burkholderia species and the close relative Ralstonia pickettii. A total of 50% of the 25 strains contained at least one of the two insertion sequences (ISs) and a statist...

journal_title：Environmental microbiology

authors： Miché L,Faure D,Blot M,Cabanne-Giuli E,Balandreau J

更新日期：2001-12-01 00:00:00

abstract：:Among human faecal bacteria, many members of the Clostridium leptum subgroup are fibrolytic and butyrate producing microorganisms thereby contributing to processes important to colonic health. Yet this phylogenetic subgroup remains poorly described to date. To improve detection and description of members of the C. lep...

journal_title：Environmental microbiology

authors： Lay C,Sutren M,Rochet V,Saunier K,Doré J,Rigottier-Gois L

更新日期：2005-07-01 00:00:00

abstract：:Assessing the extent of parasite diversity requires the application of appropriate molecular tools, especially given the growing evidence of multiple parasite co-occurrence. Here, we compared the performance of a next-generation sequencing technology (Ion PGM ™ System) in 12 Bombus terrestris specimens that were PCR-i...

journal_title：Environmental microbiology

authors： Bartolomé C,Jabal-Uriel C,Buendía-Abad M,Benito M,Ornosa C,De la Rúa P,Martín-Hernández R,Higes M,Maside X

更新日期：2021-01-01 00:00:00

abstract：:Fungi have been observed to exhibit resistance to high levels of ionizing radiation despite sharing most DNA repair mechanisms with other eukaryotes. Radioresistance, in fact, is such a common feature in fungi that it is difficult to identify species that exhibit widely different radiosensitivities, which in turn has ...

journal_title：Environmental microbiology

authors： Romsdahl J,Schultzhaus Z,Chen A,Liu J,Ewing A,Hervey J,Wang Z

更新日期：2020-10-19 00:00:00

abstract：:Fruiting body development and carotenoid production are light-induced in Cordyceps militaris. Our previous studies have shown that two blue-light receptors, CmWC-1 and CmCRY-DASH, regulate fruiting body development and secondary metabolism. However, the photosensory system of C. militaris remains unclear. Here, gene d...

journal_title：Environmental microbiology

authors： Zhang J,Wang F,Yang Y,Wang Y,Dong C

更新日期：2020-01-01 00:00:00

abstract：:Serpentinization is the hydration and oxidation of ultramafic rock, which occurs as oceanic lithosphere is emplaced onto continental margins (ophiolites), and along the seafloor as faulting exposes this mantle-derived material to circulating hydrothermal fluids. This process leads to distinctive fluid chemistries as m...

journal_title：Environmental microbiology

authors： Sabuda MC,Brazelton WJ,Putman LI,McCollom TM,Hoehler TM,Kubo MDY,Cardace D,Schrenk MO

更新日期：2020-06-01 00:00:00

abstract：:The catalase family of Beauveria bassiana (fungal entomopathogen) consists of catA (spore-specific), catB (secreted), catP (peroxisomal), catC (cytoplasmic) and catD (secreted peroxidase/catalase), which were distinguished in phylogeny and structure and functionally characterized by constructing single-gene disrupted ...

journal_title：Environmental microbiology

authors： Wang ZL,Zhang LB,Ying SH,Feng MG

更新日期：2013-02-01 00:00:00

abstract：:Tropical ecosystems remain poorly understood and this is particularly true for belowground soil fungi. Soil fungi may respond to plant identity when, for example, plants differentially allocate resources belowground. However, spatial and temporal heterogeneity in factors such as plant inputs, moisture, or nutrients ca...

journal_title：Environmental microbiology

authors： Kivlin SN,Hawkes CV

更新日期：2016-12-01 00:00:00

abstract：:We studied the vanA-carrying vancomycin-resistant enterococci (VRE) isolated from American crows in the United States during the winter 2011/2012. Faecal samples from crows were cultured selectively for VRE and characterized. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to ex...

journal_title：Environmental microbiology

authors： Oravcova V,Zurek L,Townsend A,Clark AB,Ellis JC,Cizek A,Literak I

更新日期：2014-04-01 00:00:00

abstract：:Fumarylacetoacetate hydrolase (FAH) superfamily proteins are found ubiquitously in microbial pathways involved in the catabolism of aromatic substances. Although extensive bioinformatic data on these proteins have been acquired, confusion caused by problems with the annotation of these proteins hinders research into d...

journal_title：Environmental microbiology

authors： Hong H,Seo H,Park W,Kim KJ

更新日期：2020-01-01 00:00:00

abstract：:Although bacterioplankton and phytoplankton are generally perceived as closely linked in marine systems, specific interactions between discrete bacterioplankton and phytoplankton populations are largely unknown. However, measurements of bacterioplankton distributions during phytoplankton blooms may indicate specific m...

journal_title：Environmental microbiology

authors： Morris RM,Longnecker K,Giovannoni SJ

更新日期：2006-08-01 00:00:00

abstract：:The Black Sea is the largest anoxic water basin on Earth and its stratified water column comprises an upper oxic, middle suboxic and a lower permanently anoxic, sulfidic zone. The abundance of sulfate-reducing bacteria (SRB) in water samples was determined by quantifying the copy number of the dsrA gene coding for the...

journal_title：Environmental microbiology

authors： Neretin LN,Abed RM,Schippers A,Schubert CJ,Kohls K,Kuypers MM

更新日期：2007-12-01 00:00:00

abstract：:The cattle tick Rhipicephalus (Boophilus) microplus lays eggs in the soil near the roots of grass, or in similar highly moist environments that are prone to biofilm formation. Tick eggs have a protective wax coating that may be a source of nutrients for microorganisms. However, as the eggs remain viable and show no vi...

journal_title：Environmental microbiology

authors： Zimmer KR,Macedo AJ,Giordani RB,Conceição JM,Nicastro GG,Boechat AL,Baldini RL,Abraham WR,Termignoni C

更新日期：2013-07-01 00:00:00

abstract：:Proteorhodopsin (PR) is a light-driven proton pump that has been found in a variety of marine bacteria, including Pelagibacter ubique, a member of the ubiquitous SAR11 clade. The goals of this study were to explore the diversity of PR genes and to estimate their abundance in the North Atlantic Ocean using quantitative...

journal_title：Environmental microbiology

authors： Campbell BJ,Waidner LA,Cottrell MT,Kirchman DL

更新日期：2008-01-01 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：:As part of a study on the microbiology of chlorate reduction, several new dissimilatory chlorate-reducing bacteria were isolated from a broad diversity of environments. One of these, strain CKB, was selected for a more complete characterization. Strain CKB was enriched and isolated from paper mill waste with acetate a...

journal_title：Environmental microbiology

authors： Bruce RA,Achenbach LA,Coates JD

更新日期：1999-08-01 00:00:00

abstract：:Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here, we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the...

journal_title：Environmental microbiology

authors： Robinson SL,Badalamenti JP,Dodge AG,Tassoulas LJ,Wackett LP

更新日期：2018-06-01 00:00:00

abstract：:Pseudomonas aeruginosa is a widely distributed environmental bacterium but is also an opportunistic pathogen that represents an important health hazard due to its high intrinsic antibiotic resistance and its production of virulence factors. The genetic structure of P. aeruginosa populations using whole genome sequence...

journal_title：Environmental microbiology

authors： García-Ulloa M 2nd,Ponce-Soto GY,González-Valdez A,González-Pedrajo B,Díaz-Guerrero M,Souza V,Soberón-Chávez G

更新日期：2019-08-01 00:00:00