Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses.

abstract：:The genome of the soil bacterium Pseudomonas putida strain KT2440 has been erased of various determinants of resistance to antibiotics encoded in its extant chromosome. To this end, we employed a coherent genetic platform that allowed the precise deletion of multiple genomic segments in a large variety of Gram-negativ...

journal_title：Environmental microbiology

authors： Martínez-García E,de Lorenzo V

更新日期：2011-10-01 00:00:00

abstract：:Polymicrobial bronchopulmonary infections in cystic fibrosis (CF) cause progressive lung damage and death. Although the arrival of Pseudomonas aeruginosa often heralds a more rapid rate of pulmonary decline, there is significant inter-individual variation in the rate of decline, the causes of which remain poorly under...

journal_title：Environmental microbiology

authors： Klepac-Ceraj V,Lemon KP,Martin TR,Allgaier M,Kembel SW,Knapp AA,Lory S,Brodie EL,Lynch SV,Bohannan BJ,Green JL,Maurer BA,Kolter R

更新日期：2010-05-01 00:00:00

abstract：:The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other stud...

journal_title：Environmental microbiology

authors： Jørgensen BB,Andrén T,Marshall IPG

更新日期：2020-05-01 00:00:00

abstract：:Marine sponges often harbour communities of symbiotic microorganisms that fulfil necessary functions for the well-being of their hosts. Microbial communities associated with the sponge Rhopaloeides odorabile were used as bioindicators for sublethal cupric ion (Cu2+) stress. A combined strategy incorporating molecular,...

journal_title：Environmental microbiology

authors： Webster NS,Webb RI,Ridd MJ,Hill RT,Negri AP

更新日期：2001-01-01 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：:This study presents comparative geochemical, microbiological and molecular analyses of Greenland GISP2 ice core samples representing different depths, ages, deposition climates, in situ temperatures, and gas and ionic compositions. Our goal was to determine whether specific organisms, preserved at different depths, co...

journal_title：Environmental microbiology

authors： Miteva V,Teacher C,Sowers T,Brenchley J

更新日期：2009-03-01 00:00:00

abstract：:Cultivation-independent surveys of ribosomal RNA genes have revealed the existence of novel microbial lineages, many with no known cultivated representatives. Ribosomal RNA-based analyses, however, often do not provide significant information beyond phylogenetic affiliation. Analysis of large genome fragments recovere...

journal_title：Environmental microbiology

authors： Béjà O,Suzuki MT,Koonin EV,Aravind L,Hadd A,Nguyen LP,Villacorta R,Amjadi M,Garrigues C,Jovanovich SB,Feldman RA,DeLong EF

更新日期：2000-10-01 00:00:00

abstract：:There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicr...

journal_title：Environmental microbiology

authors： Perri R,Kolvenbach BA,Corvini PFX

更新日期：2020-07-01 00:00:00

abstract：:The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and covariance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. An inter-annual pattern was delineated in the dynamic transition zone where u...

journal_title：Environmental microbiology

authors： Sudek S,Everroad RC,Gehman AL,Smith JM,Poirier CL,Chavez FP,Worden AZ

更新日期：2015-10-01 00:00:00

abstract：:Ammonia-oxidizing bacteria (AOB) have long been considered key to the removal of nitrogen in activated sludge bioreactors. Culture-independent molecular analyses have established that AOB lineages in bioreactors are dynamic, but the underlying operational or environmental factors are unclear. Furthermore, the contribu...

journal_title：Environmental microbiology

authors： Wells GF,Park HD,Yeung CH,Eggleston B,Francis CA,Criddle CS

更新日期：2009-09-01 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：:We evaluated Streptomyces biogeography in soils along a 1200 km latitudinal transect across New Zealand (NZ). Streptomyces diversity was examined using high-throughput sequencing of rpoB amplicons generated with a Streptomyces specific primer set. We detected 1287 Streptomyces rpoB operational taxonomic units (OTUs) w...

journal_title：Environmental microbiology

authors： Higgins SA,Panke-Buisse K,Buckley DH

更新日期：2020-12-07 00:00:00

abstract：:Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are com...

journal_title：Environmental microbiology

authors： McHugh TA,Morrissey EM,Mueller RC,Gallegos-Graves V,Kuske CR,Reed SC

更新日期：2017-04-01 00:00:00

abstract：:Anaerobic ammonium oxidation (anammox) is a microbial process in which NH4 (+) is oxidized to N2 gas with NO2 (-) as an electron acceptor. The anammox process is mediated by bacterial members affiliated with the phylum Planctomycetes, which are ubiquitously detected from anoxic natural and man-made ecosystems and a ke...

journal_title：Environmental microbiology

authors： Oshiki M,Satoh H,Okabe S

更新日期：2016-09-01 00:00:00

abstract：:Mercury (Hg) is a highly toxic and widely distributed heavy metal, which some Bacteria and Archaea detoxify by the reduction of ionic Hg (Hg[II]) to the elemental volatile form, Hg(0). This activity is specified by the mer operon. The mer operon of the deeply branching thermophile Thermus thermophilus HB27 encodes for...

journal_title：Environmental microbiology

authors： Norambuena J,Miller M,Boyd JM,Barkay T

更新日期：2020-04-01 00:00:00

abstract：:Diverse methylotrophic bacteria were isolated from the tongue, and supra- and subgingival plaque in the mouths of volunteers and patients with periodontitis. One-carbon compounds such as dimethylsulfide in the mouth are likely to be used as growth substrates for these organisms. Methylotrophic strains of Bacillus, Bre...

journal_title：Environmental microbiology

authors： Anesti V,McDonald IR,Ramaswamy M,Wade WG,Kelly DP,Wood AP

更新日期：2005-08-01 00:00:00

abstract：:An organism's metabolic activity leaves an extracellular footprint and dynamic changes in this exometabolome inform about nutrient uptake, waste disposal and signalling activities. Using non-targeted mass spectrometry, we report exometabolome dynamics of hypoxia-induced, non-replicating mycobacteria that are thought t...

journal_title：Environmental microbiology

authors： Zimmermann M,Kuehne A,Boshoff HI,Barry CE 3rd,Zamboni N,Sauer U

更新日期：2015-11-01 00:00:00

abstract：:Campylobacter lari is a rare human pathogen most commonly associated with birds and shellfish. Little information has been published regarding its prevalence in other environments, or on its potential role as a reservoir of antibiotic resistance. In this study, we characterized 109 C. lari isolated from a range of hos...

journal_title：Environmental microbiology

authors： Leatherbarrow AJ,Griffiths R,Hart CA,Kemp R,Williams NJ,Diggle PJ,Wright EJ,Sutherst J,Houghton P,French NP

更新日期：2007-07-01 00:00:00

abstract：:Intensive microbial growth typically observed in laboratory rarely occurs in nature. Because of severe nutrient deficiency, natural populations exhibit near-zero growth (NZG). There is a long-standing controversy about sustained NZG, specifically whether there is a minimum growth rate below which cells die or whether ...

journal_title：Environmental microbiology

authors： Panikov NS,Mandalakis M,Dai S,Mulcahy LR,Fowle W,Garrett WS,Karger BL

更新日期：2015-01-01 00:00:00

abstract：:Sub-seafloor sediments are populated by large numbers of microbial cells but not much is known about their metabolic activities, growth rates and carbon assimilation pathways. Here we introduce a new method enabling the sensitive detection of microbial lipid production and the distinction of auto- and heterotrophic ca...

journal_title：Environmental microbiology

authors： Wegener G,Bausch M,Holler T,Thang NM,Prieto Mollar X,Kellermann MY,Hinrichs KU,Boetius A

更新日期：2012-06-01 00:00:00

abstract：:Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH 4 ) and carbon dioxide (CO 2 ). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik ...

journal_title：Environmental microbiology

authors： de Jong AEE,In 't Zandt MH,Meisel OH,Jetten MSM,Dean JF,Rasigraf O,Welte CU

更新日期：2018-12-01 00:00:00

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：:Iron is the most abundant redox-active metal in the Earth's crust. The one electron transfer between the two most common redox states, Fe(II) and Fe(III), plays a role in a huge range of environmental processes from mineral formation and dissolution to contaminant remediation and global biogeochemical cycling. It has ...

journal_title：Environmental microbiology

authors： Bryce C,Blackwell N,Schmidt C,Otte J,Huang YM,Kleindienst S,Tomaszewski E,Schad M,Warter V,Peng C,Byrne JM,Kappler A

更新日期：2018-10-01 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：: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：:Fungi are important decomposers of leaf litter in streams and may have knock-on effects on other microbes and carbon cycling. To elucidate such potential effects, we designed an experiment in outdoor experimental channels simulating sand-bottom streams in an early-successional state. We hypothesized that the presence ...

journal_title：Environmental microbiology

authors： Frossard A,Gerull L,Mutz M,Gessner MO

更新日期：2012-11-01 00:00:00

abstract：:The depth distribution and diversity of sulphate-reducing bacteria (SRB) was analysed in the upper intertidal zone of a sandy marine sediment of the Dutch island Schiermonnikoog. The upper centimetre of the sediment included the oxic-anoxic interface and was cut into five slices. With each slice, most probable number ...

journal_title：Environmental microbiology

authors： Wieringa EB,Overmann J,Cypionka H

更新日期：2000-08-01 00:00:00

abstract：:Many bacterial pathogens rely on quorum sensing to control virulence gene expression. Based on numerous experiments conducted under well-defined conditions, quorum sensing interference is considered as a promising strategy to tackle infections and thus might have the potential to (partially) replace antibiotics. Despi...

journal_title：Environmental microbiology

authors： Liu Y,Qin Q,Defoirdt T

更新日期：2018-11-01 00:00:00

abstract：:To determine if different algal viruses (Phycodnaviridae) share common patterns of seasonal abundance, quantitative PCR methods were developed and applied to monitor the abundances of three different viruses in Lake Ontario, Canada over 13 months. Throughout the year, the abundances of two different phycodnavirus polB...

journal_title：Environmental microbiology

authors： Short SM,Short CM

更新日期：2009-10-01 00:00:00

abstract：:Fungi can be highly efficient biogeochemical agents and accumulators of soluble and particulate forms of metals. This work aims to understand some of the physico-chemical mechanisms involved in toxic metal transformations focusing on the speciation of metals accumulated by fungi and mycorrhizal associations. The amorp...

journal_title：Environmental microbiology

authors： Fomina M,Charnock J,Bowen AD,Gadd GM

更新日期：2007-02-01 00:00:00