Abstract:
:The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.
journal_name
Appl Environ Microbioljournal_title
Applied and environmental microbiologyauthors
Jun SR,Wassenaar TM,Nookaew I,Hauser L,Wanchai V,Land M,Timm CM,Lu TY,Schadt CW,Doktycz MJ,Pelletier DA,Ussery DWdoi
10.1128/AEM.02612-15subject
Has Abstractpub_date
2015-10-30 00:00:00pages
375-83issue
1eissn
0099-2240issn
1098-5336pii
AEM.02612-15journal_volume
82pub_type
杂志文章abstract::Erwinia amylovora bacteriophages (phages) belonging to the Myoviridae and Podoviridae families demonstrated a preference for either high-exopolysaccharide-producing (HEP) or low-exopolysaccharide-producing (LEP) bacterial hosts when grown on artificial medium without or with sugar supplementation. Myoviridae phages pr...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00067-13
更新日期:2013-05-01 00:00:00
abstract::Inactivation of aflatoxin B1 was studied by using gamma radiation and hydrogen peroxide. A 100-krad dose of gamma radiation was sufficient to inactivate 50 micrograms of aflatoxin B1 in the presence of 5% hydrogen peroxide, and 400 krad was required for total degradation of 100 micrograms of aflatoxin in the same syst...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.55.2.465-467.1989
更新日期:1989-02-01 00:00:00
abstract::The thermophilic homoacetogenic bacterium Moorella sp. strain HUC22-1 ferments glyoxylate to acetate roughly according to the reaction 2 glyoxylate --> acetate + 2 CO(2). A batch culture with glyoxylate and yeast extract yielded 11.7 g per mol of cells per substrate, which was much higher than that obtained with H(2) ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01421-07
更新日期:2008-03-01 00:00:00
abstract::n-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of n-alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. Th...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01447-17
更新日期:2017-10-17 00:00:00
abstract::Eight concentration and purification methods were evaluated to determine percentages of recovery of Cryptosporidium parvum oocysts from calf feces. The NaCl flotation method generally resulted in the highest percentages of recovery. Based on the percentages of recovery, the amounts of fecal debris in the final oocyst ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.65.7.2820-2826.1999
更新日期:1999-07-01 00:00:00
abstract::Infections caused by Toxoplasma gondii are widely prevalent in animals and humans throughout the world. In the United States, an estimated 23% of adolescents and adults have laboratory evidence of T. gondii infection. T. gondii has been identified as a major opportunistic pathogen in immunocompromised individuals, in ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.69.10.5819-5825.2003
更新日期:2003-10-01 00:00:00
abstract::Aerobic biotransformation of the diaryl ethers 2,7-dichlorodibenzo-p-dioxin and 1,2,3,4-tetrachlorodibenzo-p-dioxin by the dibenzo-p-dioxin-utilizing strain Sphingomonas wittichii RW1, producing corresponding metabolites, was demonstrated for the first time. Our strain transformed 2,7-dichlorodibenzo-p-dioxin, yieldin...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.68.5.2584-2588.2002
更新日期:2002-05-01 00:00:00
abstract::The design of fully or partly defined media for mycoplasma cultivation involves the need to provide the essential lipids, cholesterol and long-chain fatty acids, in an assimilable and nontoxic form. This study introduces cyclodextrins (CDs) as carriers of these lipids, thus suggesting alternatives to serum or bovine s...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.59.2.547-551.1993
更新日期:1993-02-01 00:00:00
abstract::The natural products of both eremofortin C (EC) and PR toxin are secondary metabolites of Penicillium roqueforti. Because the chemical structures of EC and PR toxin are closely related to each other and differ only by a hydroxyl functional group in EC and an aldehyde functional group in PR toxin at the C-12 position, ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.50.3.729-731.1985
更新日期:1985-09-01 00:00:00
abstract::The N-acetylglucosaminidase LytB of Streptococcus pneumoniae is involved in nasopharyngeal colonization and is responsible for cell separation at the end of cell division; thus, ΔlytB mutants form long chains of cells. This paper reports the construction and properties of a defective pneumococcal mutant producing an i...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00280-20
更新日期:2020-05-05 00:00:00
abstract::The capacity of polycyclic aromatic hydrocarbon (PAH)-utilizing bacteria to produce biosurfactants was investigated. Twenty-three bacteria isolated from a soil contaminated with petroleum wastes were able to form clearing zones on mineral salt agar plates sprayed with solutions of PAHs. Naphthalene and phenanthrene we...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.62.6.1908-1912.1996
更新日期:1996-06-01 00:00:00
abstract::Fifteen Bacillus thuringiensis strains representing 13 serotypes were screened with five oligodeoxyribonucleotide probes specific for certain regions of two published sequences and one unpublished sequence of B. thuringiensis delta-endotoxin genes. Of the 15 cultures, 14 hybridized with at least one probe; the B. thur...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.53.12.2808-2814.1987
更新日期:1987-12-01 00:00:00
abstract::This research documents an effect of reactor turbulence on the ability of gram-negative wastewater biofilm bacteria to actively transport l-aspartate via a binding-protein-mediated transport system. Biofilms which were not preadapted to turbulence and which possessed two separate and distinct aspartate transport syste...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.50.1.120-124.1985
更新日期:1985-07-01 00:00:00
abstract::The response of Lactobacillus delbrueckii subsp. bulgaricus cells to heat stress was studied by use of a chemically defined medium. Two-dimensional electrophoresis (2-DE) analysis was used to correlate the kinetics of heat shock protein (HSP) induction with cell recovery from heat injury. We demonstrated that enhanced...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.68.3.1055-1063.2002
更新日期:2002-03-01 00:00:00
abstract::The effects of Cd2+, Cu2+, Mg2+, and Zn2+ on the decomposition of citric acid by a Klebsiella sp. were studied by monitoring the degradation of [14C]citrate. The carbon concentration used was 10 micrograms of C liter-1, and the media were designed to provide at least 95% of the citrate complexed to the metal studied. ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.55.6.1375-1379.1989
更新日期:1989-06-01 00:00:00
abstract::This study concerns the exploitation of the lytic enzyme enterolysin A (EntL), produced by Enterococcus faecalis strain DPC5280, to elicit the controlled autolysis of starter lactococci. EntL, a cell wall metalloendopeptidase secreted by some E. faecalis strains, can kill a wide range of gram-positive bacteria, includ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.70.3.1744-1748.2004
更新日期:2004-03-01 00:00:00
abstract::Culture-independent (PCR with Crenarchaeota-specific primers and subsequent denaturing gradient gel electrophoresis) and culture-dependent approaches were used to study the diversity of Crenarchaeota in terrestrial hot springs of the Kamchatka Peninsula and the Lake Baikal region (Russia) and of Iceland. Among the phy...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00972-08
更新日期:2008-12-01 00:00:00
abstract::Legionella pneumophila suspended in tap water was exposed to biocides recommended for inhibiting biological growth in cooling towers and evaporative condensers of air-conditioning systems. Chlorine, 2,2-dibromo-3-nitrilopropionamide, and a compound containing didecyldimethylammonium chloride and isopropanol were effec...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.40.4.697-700.1980
更新日期:1980-10-01 00:00:00
abstract::The antimicrobial activities of sucrose monolaurate and a novel ester, lactose monolaurate (LML), were tested. Gram-positive bacteria were more susceptible than Gram-negative bacteria to both esters. The minimal bactericidal concentrations of LML were 5 to 9.5 mM for Listeria monocytogenes isolates and 0.2 to 2 mM for...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.07701-11
更新日期:2012-05-01 00:00:00
abstract::Cotton flowers in replicate plots in two fields near Phoenix, Ariz., were tagged in June at the beginning of the flowering period. Flowers or developing bolls from these tagged flowers were inoculated on the involucral (bracteal) nectaries with dry spores of Aspergillus flavus. The bolls were harvested as they matured...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.50.3.602-604.1985
更新日期:1985-09-01 00:00:00
abstract::The enrichment and isolation of thermophilic bacteria capable of rubber [poly(cis-1,4-isoprene)] degradation revealed eight different strains exhibiting both currently known strategies used by rubber-degrading mesophilic bacteria. Taxonomic characterization of these isolates by 16S rRNA gene sequence analysis demonstr...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.72.5.3375-3382.2006
更新日期:2006-05-01 00:00:00
abstract::Estimations of the bacterial content of air can be more easily made now than a decade ago, with colony formation the method of choice for enumeration of airborne bacteria. However, plate counts are subject to error because bacteria exposed to the air may remain viable yet lose the ability to form colonies, i.e., they ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.63.9.3585-3588.1997
更新日期:1997-09-01 00:00:00
abstract::In the present work, we aimed at determining the relationship between the hepatitis A virus (HAV) numbers in imported frozen coquina clams involved in two hepatitis outbreaks, as well as the risk for human health. Due to HAV unculturability, a standardized TaqMan real-time reverse transcription-PCR controlling the vir...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01177-09
更新日期:2009-12-01 00:00:00
abstract::A simple synthetic liquid medium containing a single amino acid, glucose, salts, trace metals, and thiamine was developed for cultivation of Cercospora rosicola Passerini. Thiamine was shown to be important to growth. Culture of C. rosicola Passerini in a chemically defined medium makes possible studies of (+)-abscisi...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.41.1.334-336.1981
更新日期:1981-01-01 00:00:00
abstract::A gene encoding a putative 150-amino-acid methylglyoxal synthase was identified in Clostridium acetobutylicum ATCC 824. The enzyme was overexpressed in Escherichia coli and purified. Methylglyoxal synthase has a native molecular mass of 60 kDa and an optimum pH of 7.5. The Km and Vmax values for the substrate dihydrox...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.65.7.3244-3247.1999
更新日期:1999-07-01 00:00:00
abstract::The ammonia-oxidizing prokaryote (AOP) community in three groundwater treatment plants and connected distribution systems was analyzed by quantitative real-time PCR and sequence analysis targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Results demonstrated that AOB and AOA numbers increas...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00387-09
更新日期:2009-07-01 00:00:00
abstract::The conversion of ochratoxin C to ochratoxin A was studied in rats after oral and intravenous administration. The concentration of ochratoxin A in the blood as a function of time was the same after oral administration of equivalent amounts of either ochratoxin C or ochratoxin A. The maximum ochratoxin A concentrations...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.48.1.41-42.1984
更新日期:1984-07-01 00:00:00
abstract::The expression of xenobiotic-degradative genes in indigenous bacteria or in bacteria introduced into an ecosystem is essential for the successful bioremediation of contaminated environments. The maintenance of naphthalene utilization activity is studied in Pseudomonas putida (ATCC 17484) and an Alcaligenes sp. (strain...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.61.11.4061-4068.1995
更新日期:1995-11-01 00:00:00
abstract::A new design, flat-bottom combination pH electrode was evaluated for utility in determining the pH of prepared agar media by surface contact of the electrode with the agar media. ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.34.2.242-243.1977
更新日期:1977-08-01 00:00:00
abstract::This is the first study to characterize the environmental conditions which contribute to the presence and proliferation of environmental mycobacteria in a major freshwater river. Over 20 different species of environmental mycobacteria were isolated, including the pathogenic M. avium and M. kansasii. Species of the rap...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.71.10.5719-5727.2005
更新日期:2005-10-01 00:00:00