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You searched for: Journal Environmental microbiology Remove constraint Journal: Environmental microbiology Publication Year 2008 Remove constraint Publication Year: 2008 Source 2008 v.10 no.2 Remove constraint Source: 2008 v.10 no.2
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1. Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids

Author:
Shrestha, Minita; Abraham, Wolf-Rainer; Shrestha, Pravin Malla; Noll, Matthias; Conrad, Ralf
Source:
Environmental microbiology 2008 v.10 no.2 pp. 400-412
ISSN:
1462-2912
Subject:
fatty acids; greenhouse gases; rice; genes; roots; stable isotopes; rhizosphere; bacterial communities; oxidation; ecosystems; phospholipids; restriction fragment length polymorphism; temporal variation; community structure; soil sampling; emissions; methanotrophs; paddies; population size; rice soils; methane; nucleotide sequences
Abstract:
... Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH₄ into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH₄ flux in the presence and absence of d ...
DOI:
10.1111/j.1462-2920.2007.01462.x
PubMed:
18177369

2. Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica

Author:
Finsinger, Karin; Scholz, Ingeborg; Serrano, Aurelio; Morales, Saylen; Uribe-Lorio, Lorena; Mora, Marielos; Sittenfeld, Ana; Weckesser, Jürgen; Hess, Wolfgang R.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 460-473
ISSN:
1462-2912
Subject:
Fischerella muscicola; Mastigocladus laminosus; biodiversity; genes; intergenic DNA; phylogeny; ribosomal RNA; spring; subtropics; transfer RNA; Costa Rica
Abstract:
... Costa Rica is at the centre of the Mesoamerican biodiversity hotspot. Little is known about cyanobacteria from this region so far. Here, four isolates of the order Stigonematales (section V) were characterized in a polyphasic approach. All strains were isolated from geothermal sites and hot springs of Costa Rica. However, one of them, identified as Westiellopsis sp. Ar73, did not grow at more than ...
DOI:
10.1111/j.1462-2920.2007.01467.x
PubMed:
18093164

3. Design and testing of 'genome-proxy' microarrays to profile marine microbial communities

Author:
Rich, Virginia I.; Konstantinidis, Konstantinos; DeLong, Edward F.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 506-521
ISSN:
1462-2912
Subject:
DNA; Prochlorococcus; clones; coastal water; genes; genomic libraries; genotype; microarray technology; microbial communities; oceans; open reading frames; phylogeny; prototypes; Antarctic region; Hawaii
Abstract:
... Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a 'genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted o ...
DOI:
10.1111/j.1462-2920.2007.01471.x
PubMed:
18028413

4. Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses

Author:
Chen, Yin; Dumont, Marc G.; McNamara, Niall P.; Chamberlain, Paul M.; Bodrossy, Levente; Stralis-Pavese, Nancy; Murrell, J. Colin
Source:
Environmental microbiology 2008 v.10 no.2 pp. 446-459
ISSN:
1462-2912
Subject:
Calluna vulgaris; Methylocella; Methylocystis; community structure; fatty acids; gamma-Proteobacteria; genes; habitats; heathlands; messenger RNA; methane; methanotrophs; microarray technology; oxidation; peatlands; soil; soil sampling; United Kingdom
Abstract:
... The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH₄ oxidation ...
DOI:
10.1111/j.1462-2920.2007.01466.x
PubMed:
18093158

5. Diversity responses of rumen microbial communities to Fusarium-contaminated feed, evaluated with rumen simulating technology

Author:
Strobel, Egbert; Seeling, Karen; Tebbe, Christoph C.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 483-496
ISSN:
1462-2912
Subject:
Clostridiales; Fusarium culmorum; bacteria; deoxynivalenol; feed contamination; feeds; fungi; genes; livestock; microbial communities; nutrients; polymerase chain reaction; ribosomal RNA; rumen; single-stranded conformational polymorphism; spoilage
Abstract:
... The mycotoxin-producing fungus Fusarium culmorum causes major feed spoilages in agricultural livestock, but effects of F. culmorum-contaminated feed on the structural diversity of the rumen-inhabiting microbial community are not understood. Avoiding animal experiments, this study was conducted with the rumen simulating technique (Rusitec). Small subunit (SSU) rRNA gene copy numbers of bacteria and ...
DOI:
10.1111/j.1462-2920.2007.01469.x
PubMed:
18177368

6. Fluorescent properties of c-type cytochromes reveal their potential role as an extracytoplasmic electron sink in Geobacter sulfurreducens

Author:
Esteve-Núñez, Abraham; Sosnik, Julian; Visconti, Pablo; Lovley, Derek R.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 497-505
ISSN:
1462-2912
Subject:
Geobacter sulfurreducens; absorbance; biofilm; chemical reduction; cytochromes; electron transfer; electrons; energy requirements; flagellum; fluorescence; fluorescence microscopy; heme; iron; iron oxides; monitoring; oxidation; protons; viability; wavelengths
Abstract:
... A novel fluorescence technique for monitoring the redox status of c-type cytochromes in Geobacter sulfurreducens was developed in order to evaluate the capacity of these extracytoplasmic cytochromes to store electrons during periods in which an external electron acceptor is not available. When intact cells in which the cytochromes were in a reduced state were excited at a wavelength of 350 nm, the ...
DOI:
10.1111/j.1462-2920.2007.01470.x
PubMed:
18093163

7. Genes encoding the candidate enzyme for anaerobic activation of n-alkanes in the denitrifying bacterium, strain HxN1

Author:
Grundmann, Olav; Behrends, Astrid; Rabus, Ralf; Amann, Judith; Halder, Thomas; Heider, Johann; Widdel, Friedrich
Source:
Environmental microbiology 2008 v.10 no.2 pp. 376-385
ISSN:
1462-2912
Subject:
Northern blotting; amino acid sequences; beta-Proteobacteria; denitrification; denitrifying bacteria; enzymes; hexane; multigene family; nucleic acid hybridization; operon; phylogeny; protein subunits; transcription (genetics); two-dimensional gel electrophoresis
Abstract:
... Strain HxN1, a member of the Betaproteobacteria, can grow anaerobically by denitrification with n-alkanes. n-Alkanes are apparently activated by subterminal carbon addition to fumarate yielding (1-methylalkyl)succinates, the postulated enzyme being (1-methylalkyl)succinate synthase (Mas). Genes encoding this enzyme (mas) were searched for via proteins that were specifically formed in n-hexane-grow ...
DOI:
10.1111/j.1462-2920.2007.01458.x
PubMed:
17961174

8. Genetic analyses and molecular characterization of the pathways involved in the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid in Pseudomonas putida U

Author:
Arias, Sagrario; Olivera, Elías R.; Arcos, Mario; Naharro, Germán; Luengo, José M.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 413-432
ISSN:
1462-2912
Subject:
Escherichia coli; Pseudomonas putida; alcohol dehydrogenase; aldehyde dehydrogenase; amines; binding proteins; biosynthesis; catalytic activity; cytochrome c; deamination; electron transfer; genetic techniques and protocols; oxidation; phenylacetaldehyde; phenylacetic acid
Abstract:
... In Pseudomonas putida U two different pathways (Pea, Ped) are required for the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid. The 2-phenylethylamine pathway (PeaABCDEFGHR) catalyses the transport of this amine, its deamination to phenylacetaldehyde by a quinohaemoprotein amine dehydrogenase and the oxidation of this compound through a reaction catalysed by a phenylace ...
DOI:
10.1111/j.1462-2920.2007.01464.x
PubMed:
18177365

9. Genotypic variability and persistence of Legionella pneumophila PFGE patterns in 34 cooling towers from two different areas

Author:
Sanchez, Inma; Garcia-Nuñez, Marian; Ragull, Sonia; Sopena, Nieves; Pedro-Botet, Maria Luisa; Estere, Maria; Rey-Joly, Celestino; Sabria, Miquel
Source:
Environmental microbiology 2008 v.10 no.2 pp. 395-399
ISSN:
1462-2912
Subject:
Legionella pneumophila; clonal variation; cooling; molecular epidemiology; outbreak investigation; pulsed-field gel electrophoresis
Abstract:
... Genotypic variability and clonal persistence are important concepts in molecular epidemiology as they facilitate the search for the source of sporadic cases or outbreaks of legionellosis. We studied the genotypic variability and persistence of Legionella pulsed-field gel electrophoresis (PFGE) patterns over time (period > 6 months) in 34 positive cooling towers from two different areas. In area A, ...
DOI:
10.1111/j.1462-2920.2007.01460.x
PubMed:
18199124

10. Identification and analysis of a glutaryl-CoA dehydrogenase-encoding gene and its cognate transcriptional regulator from Azoarcus sp. CIB

Author:
Blázquez, Blas; Carmona, Manuel; García, José Luis; Díaz, Eduardo
Source:
Environmental microbiology 2008 v.10 no.2 pp. 474-482
ISSN:
1462-2912
Subject:
Azoarcus; Pseudomonas putida; amino acid sequences; aromatic compounds; dicarboxylic acids; gene expression; metabolism; phylogeny; promoter regions; regulator genes; transcription (genetics)
Abstract:
... In this work, the gcdH gene from the denitrifying β-proteobacterium Azoarcus sp. CIB was shown to encode a glutaryl-CoA dehydrogenase, which is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The primary structure of the GcdH protein is highly conserved in many organisms. The divergently transcribed gcdR gene, encoding a LysR-type transc ...
DOI:
10.1111/j.1462-2920.2007.01468.x
PubMed:
18177371

11. Manure-amended soil characteristics affecting the survival of E. coli O157:H7 in 36 Dutch soils

Author:
Franz, Eelco; Semenov, Alexander V.; Termorshuizen, Aad J.; de Vos, O.J.; Bokhorst, Jan G.; van Bruggen, Ariena H.C.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 313-327
ISSN:
1462-2912
Subject:
Escherichia coli O157; Weibull statistics; animal manures; arable soils; composted manure; denaturing gradient gel electrophoresis; detection limit; dissolved organic carbon; dissolved organic nitrogen; foodborne illness; loam soils; organic soils; population dynamics; raw vegetables; risk factors; sandy soils; soil quality; species diversity
Abstract:
... The recent increase in foodborne disease associated with the consumption of fresh vegetables stresses the importance of the development of intervention strategies that minimize the risk of preharvest contamination. To identify risk factors for Escherichia coli O157:H7 persistence in soil, we studied the survival of a Shiga-toxin-deficient mutant in a set of 36 Dutch arable manure-amended soils (or ...
DOI:
10.1111/j.1462-2920.2007.01453.x
PubMed:
18199123

12. Microbial distribution of Accumulibacter spp. and Competibacter spp. in aerobic granules from a lab-scale biological nutrient removal system

Author:
Lemaire, Romain; Yuan, Zhiguo; Blackall, Linda L.; Crocetti, Gregory R.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 354-363
ISSN:
1462-2912
Subject:
bacteria; biomass; carbon; denitrification; fluorescence in situ hybridization; glycogen; granules; microbial communities; nitrification; oxygen; phosphorus; sludge
Abstract:
... Granular sludge for simultaneous nitrification, denitrification and phosphorus removal (SNDPR) was generated and studied in a lab-scale sequencing batch reactor (SBR). The SBR was monitored for 450 days during which the biomass was transformed from flocs to granules, which persisted for the last 130 days of operation. Short sludge settling time was employed to successfully generate the granules, w ...
DOI:
10.1111/j.1462-2920.2007.01456.x
PubMed:
18028415

13. Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans

Author:
Fekete, Csaba; Tholander, Margareta; Rajashekar, Balaji; Ahrén, Dag; Friman, Eva; Johansson, Tomas; Tunlid, Anders
Source:
Environmental microbiology 2008 v.10 no.2 pp. 364-375
ISSN:
1462-2912
Subject:
Caenorhabditis elegans; RNA; antimicrobial peptides; complementary DNA; hosts; lectins; microarray technology; nematophagous fungi; paralysis; proteinase inhibitors; reporter genes; transcriptome; traps
Abstract:
... The transcriptional response in the parasitic fungus Monacrosporium haptotylum and its nematode host Caenorhabditis elegans were analysed during infection using cDNA microarrays. The array contained 2684 fungal and 372 worm gene reporters. Dramatic shifts occurred in the transcriptome of M. haptotylum during the different stages of the infection. An initial transcriptional response was recorded af ...
DOI:
10.1111/j.1462-2920.2007.01457.x
PubMed:
18028414

14. Polysaccharide hydrolysis in aggregates and free enzyme activity in aggregate-free seawater from the north-eastern Gulf of Mexico

Author:
Ziervogel, Kai; Arnosti, Carol
Source:
Environmental microbiology 2008 v.10 no.2 pp. 289-299
ISSN:
1462-2912
Subject:
bacteria; carbon; cell aggregates; enzymatic hydrolysis; enzyme activity; enzymes; fluorescent labeling; hydrolysis; lipids; microscopy; molecular weight; oceans; polysaccharides; proteins; seawater; water activity; Gulf of Mexico
Abstract:
... Marine snow aggregates represent hotspots of carbon remineralization in the ocean. Various aspects of bacterial dynamics have been investigated on marine snow. To date, extracellular enzymatic activities in aggregates have been measured using small substrate proxies that do not adequately reflect the complexity of biomacromolecules such as polysaccharides, proteins and lipids. To address this issu ...
DOI:
10.1111/j.1462-2920.2007.01451.x
PubMed:
18093165

15. Prevalence of highly host-specific cyanophages in the estuarine environment

Author:
Wang, Kui; Chen, Feng
Source:
Environmental microbiology 2008 v.10 no.2 pp. 300-312
ISSN:
1462-2920
Subject:
DNA; DNA-directed DNA polymerase; Prochlorococcus; Synechococcus; bacteriophages; ecosystems; estuaries; genes; host range; host specificity; oceans; photosynthesis
Abstract:
... Cyanophages that infect coastal and oceanic Synechococcus have been studied extensively. However, no cyanophages infecting estuarine Synechococcus have been reported. In this study, seven cyanophages (three podoviruses, three siphoviruses and one myovirus) isolated from four estuarine Synechococcus strains were characterized in terms of their morphology, host range, growth and genetic features. Al ...
DOI:
10.1111/j.1462-2920.2007.01452.x
PubMed:
17900294

16. Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots

Author:
Singh, Brajesh K.; Nunan, Naoise; Ridgway, Karyn P.; McNicol, Jim; Young, J. Peter W.; Daniell, Tim J.; Prosser, James I.; Millard, Peter
Source:
Environmental microbiology 2008 v.10 no.2 pp. 534-541
ISSN:
1462-2912
Subject:
DNA; botanical composition; fungal communities; genes; grasses; mycorrhizal fungi; pastures; restriction fragment length polymorphism; rhizoplane; ribosomal RNA; roots; soil bacteria; soil pH; vesicular arbuscular mycorrhizae
Abstract:
... Soils support an enormous microbial diversity, but the ecological drivers of this diversity are poorly understood. Interactions between the roots of individual grass species and the arbuscular mycorrhizal (AM) fungi and bacteria in their rhizoplane were studied in a grazed, unimproved upland pasture. Individual root fragments were isolated from soil cores, DNA extracted and used to identify plant ...
DOI:
10.1111/j.1462-2920.2007.01474.x
PubMed:
18081854

17. Responses of aerobic microbial communities and soil respiration to water-level drawdown in a northern boreal fen

Author:
Jaatinen, Krista; Laiho, Raija; Vuorenmaa, Anita; del Castillo, Urko; Minkkinen, Kari; Pennanen, Taina; Penttilä, Timo; Fritze, Hannu
Source:
Environmental microbiology 2008 v.10 no.2 pp. 339-353
ISSN:
1462-2912
Subject:
Actinobacteria; air temperature; biomass; carbon; dry forests; ectomycorrhizae; fatty acids; fens; fungal communities; fungi; groundwater extraction; peat; peatlands; phospholipids; prediction; soil microorganisms; soil respiration
Abstract:
... On a global basis, peatlands are a major reserve of carbon (C). Hydrological changes can affect the decomposition processes in peatlands and in turn can alter their C balance. Since 1959, a groundwater extraction plant has generated a water-level gradient at our study site that has gradually changed part of the wet fen into a dry peatland forest. The average water-level drawdown of the gradient (f ...
DOI:
10.1111/j.1462-2920.2007.01455.x
PubMed:
17903215

18. Role of the metalloprotease Vvp and the virulence plasmid pR99 of Vibrio vulnificus serovar E in surface colonization and fish virulence

Author:
Valiente, Esmeralda; Lee, Chung-Te; Hor, Lien-I.; Fouz, Belén; Amaro, Carmen
Source:
Environmental microbiology 2008 v.10 no.2 pp. 328-338
ISSN:
1462-2912
Subject:
Vibrio vulnificus; eel; chemoattractants; mucins; septicemia; serotypes; mutation; aquatic environment; biotypes; mucus; genes; gills; blood; virulence
Abstract:
... The virulence for eels of Vibrio vulnificus biotype 2 serovar E (VSE) is conferred by a plasmid that codifies ability to survive in eel serum and cause septicaemia. To find out whether the plasmid and the selected chromosomal gene vvp plays a role in the initial steps of infection, the VSE strain CECT4999, the cured strain CT218 and the Vvp-deficient mutant CT201 (obtained in this work by allelic ...
DOI:
10.1111/j.1462-2920.2007.01454.x
PubMed:
18028416

19. Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat

Author:
Smith, Jason M.; Green, Stefan J.; Kelley, Cheryl A.; Prufert-Bebout, Leslie; Bebout, Brad M.
Source:
Environmental microbiology 2008 v.10 no.2 pp. 386-394
ISSN:
1462-2912
Subject:
Methanomicrobiales; Methanosarcinales; biochemical pathways; clones; community structure; genes; greenhouses; methane; methane production; methanogens; salinity; sulfates; California; Mexico
Abstract:
... Methanogenesis was characterized in hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico both in situ and after long-term manipulation in a greenhouse environment. Substrate addition experiments indicate methanogenesis to occur primarily through the catabolic demethylation of non-competitive substrates, under field conditions. However, evidence for the coexistence of other m ...
DOI:
10.1111/j.1462-2920.2007.01459.x
PubMed:
18177370

20. The role of the nitrate respiration element of Thermus thermophilus in the control and activity of the denitrification apparatus

Author:
Cava, Felipe; Zafra, Olga; da Costa, Milton S.; Berenguer, José
Source:
Environmental microbiology 2008 v.10 no.2 pp. 522-533
ISSN:
1462-2912
Subject:
NAD (coenzyme); Thermus thermophilus; aerobiosis; denitrification; electrons; enzymes; mutants; nitrate reduction; nitrates; nitrites; oxidation; transcription factors
Abstract:
... The nitrate conjugative element (NCE) encodes the ability to respire nitrate in the facultative Thermus thermophilus NAR1 strain. This process is carried out by two heterotetrameric enzymes that catalyse the oxidation of NADH (Nrc) and the reduction of nitrate (Nar), whose expression is activated by the NCE-encoded transcription factors DnrS and DnrT. We report the presence of NCE in other faculta ...
DOI:
10.1111/j.1462-2920.2007.01472.x
PubMed:
18199125