bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of sociality on the conservation biology of social insects
Authors: Chapman Roselle E. , Bourke Andrew F. G.
Published: March 2003

Social insects (ants, bees, wasps and termites) as a group are species rich and ecologically dominant. Many are outstanding “ecological engineers”, or providers of “ecosystem services”, or potential bioindicator species. Few social insects are currently formally classified as Threatened, but this is almost certainly due to a lack of information on population sizes and trends in scarce species. The main influence that sociality has on threats faced by social insects is in reducing effective population sizes, increasing population genetic subdivision and possibly reducing levels of genetic variation relative to solitary species. The main influence that sociality has on threats from social insects is via its role in the ecological success of invasive species, which frequently pose a major hazard to native biotas. In some cases, social features underpinning ecological success in the original range almost certainly contribute to the success of invasive social insects. However, recent studies show or strongly suggest that, in some of the most notoriously invasive populations of ants, bees and wasps, novel social traits have arisen that greatly enhance the rate of spread and ecological competitiveness of these populations. Sociality can therefore represent either a liability or an asset in its contribution to the persistence of social insect populations.
Natural adaptation to environmental stress via physiological clock‐regulation of stress resistance in Drosophila
Authors: Sørensen Jesper Givskov , Loeschcke Volker
Published: March 2003

In the present study we describe a novel mechanism by which populations, in an interplay between physiology and behaviour, can evolve adaptation to environmental extremes. Comparing Drosophila populations from different climate zones, we found diel shifts in high temperature resistance after maintenance at 25 °C for several generations. Resistance changes that co‐occurred with field and laboratory activity of the populations are controlled by the physiological clock and appear to be a consequence of local adaptation to the thermal profiles of the environment of origin.
Stoichiometry of nutrient recycling by vertebrates in a tropical stream: linking species identity and ecosystem processes
Authors: Vanni Michael J. , Flecker Alexander S. , Hood James M. , Headworth Jenifer L.
Published: March 2003

Ecological stoichiometry offers a framework for predicting how animal species vary in recycling nutrients, thus providing a mechanism for how animal species identity mediates ecosystem processes. Here we show that variation in the rates and ratios at which 28 vertebrate species (fish, amphibians) recycled nitrogen (N) and phosphorus (P) in a tropical stream supports stoichiometry theory. Mass‐specific P excretion rate varied 10‐fold among taxa and was negatively related to animal body P content. In addition, the N : P ratio excreted was negatively related to body N : P. Body mass (negatively related to excretion rates) explained additional variance in these excretion parameters. Body P content and P excretion varied much more among taxonomic families than among species within families, suggesting that familial composition may strongly influence ecosystem‐wide nutrient cycling. Interspecific variation in nutrient recycling, mediated by phylogenetic constraints on stoichiometry and allometry, illustrates a strong linkage between species identity and ecosystem function.
Dynamics of anoxygenic photosynthesis in an experimental green sulphur bacteria biofilm
Authors: Pringault Olivier , Epping Eric , Guyoneaud Remy , Khalili Arzhang , Kühl Michael
Published: March 2003

The dynamics of sulphide oxidation in an experimental biofilm of the green sulphur bacterium, Prosthecochloris aestuarii, were studied using a newly developed light–dark cycling procedure. The biofilm was grown for 6 weeks in a benthic gradient chamber, in which gradients of light, sulphide and oxygen were imposed experimentally. The H2S concentrations and pH were measured with microsensors as a function of depth in the biofilm and of time after a change in illumination status. The sulphide oxidation rates were calculated as a function of time and depth in the biofilm using a numerical procedure to solve the non‐stationary general diffusion equation. A close agreement was found between the areal rates of anoxygenic photosynthesis during the cycling procedure and the steady state before the cycling experiment. For the different layers of the biofilm, the maximum activity was observed after 10–12 min of light exposure. After this maximum, sulphide oxidation decreased concomitantly with sulphide concentration, indicating sulphide limitation of anoxygenic photosynthesis. This lag time limits the application of the standard dark–light shift method with a brief light exposure of a few seconds and, therefore, the numerical procedure described in this study enables the depth distribution of anoxygenic photosynthesis rates in microbial mats to be determined more accurately.
Host specificity in the Richelia–diatom symbiosis revealed by hetR gene sequence analysis
Authors: Janson  , Wouters  , Bergman  , Carpenter
Published: March 2003

The filamentous heterocyst‐forming cyanobacterium Richelia intracellularis forms associations with diatoms and is very abundant in tropical and subtropical seas. The genus Richelia contains only one species, R. intracellularis Schmidt, although it forms associations with several diatom genera and has considerable variation in size and morphology. The genetic diversity, and possible host specificity, within the genus Richelia is unknown. Using primers against hetR, a gene unique for filamentous cyanobacteria, specific polymerase chain reaction (PCR) products were obtained from natural populations of R. intracellularis filaments associated with three diatom genera. Phylogenetic analyses of these sequences showed that they were all in the same clade. This clade contained only the R. intracellularis sequences. The genetic affiliation of hetR sequences of R. intracellularis to those of other heterocystous cyanobacteria strongly suggests that it was not closely related to endosymbiotic Nostoc spp. hetR sequences. Sequences from R. intracellularis–Hemiaulus membranaceus sampled in the Atlantic and Pacific Oceans were almost identical, demonstrating that the genetic relatedness was not dependent on geographical location. All sequences displayed a deep divergence between symbionts from different genera and a high degree of host specificity.
Mannuronan C‐5 epimerases and cellular differentiation of Azotobacter vinelandii
Authors: Høidal Hilde Kristin , Svanem Britt Iren Glærum , Gimmestad Martin , Valla Svein
Published: March 2003

Differentiation in Azotobacter vinelandii involves the encystment of the vegetative cell under adverse environmental circumstances and the germination of the resting cell into the vegetative state when growth conditions are satisfactory again. Morphologically, the encystment process involves the development of a protective coat around the resting cell. This coat partly consists of multiple layers of alginate, which is a co‐polymer of β‐
d‐mannuronic acid (M) and α‐
l‐guluronic acid (G). Alginate contributes to coat rigidity by virtue of a high content of GG blocks. Such block structures are generated through a family of mannuronan C‐5 epimerases that convert M to G after polymerization. Results from immunodetection and light microscopy, using stains that distinguish between different cyst components and types, indicate a correlation between cyst coat organization and the amount and appearance of mannuronan C‐5 epimerases in the extracellular medium and attached to the cells. Specific roles of individual members of the epimerase family are indicated. Calcium and magnesium ions appear to have different roles in the structural organization of the cyst coat. Also reported is a new gene sharing strong sequence homology with parts of the epimerase‐encoded R‐modules. This gene is located within the epimerase gene cluster of Azotobacter vinelandii.
Role of commensal relationships on the spatial structure of a surface‐attached microbial consortium
Authors: Nielsen Alex T. , Tolker‐Nielsen Tim , Barken Kim B. , Molin Søren
Published: March 2003

A flow cell‐grown model consortium consisting of two organisms, Burkholderia sp. LB400 and Pseudomonas sp. B13(FR1), was studied. These bacteria have the potential to interact metabolically because Pseudomonas sp. B13(FR1) can metabolize chlorobenzoate produced by Burkholderia sp. LB400 when grown on chlorobiphenyl. The expected metabolic interactions in the consortium were demonstrated by high performance liquid chromatography (HPLC) analysis. The spatial structure of the consortium was studied by fluorescent in situ rRNA hybridization and scanning confocal laser microscopy. When the consortium was fed with medium containing a low concentration of chlorobiphenyl, microcolonies consisting of associated Burkholderia sp. LB400 and Pseudomonas sp. B13(FR1) bacteria were formed, and separate Pseudomonas sp. B13(FR1) microcolonies were evidently not formed. When the consortium was fed citrate, which can be metabolized by both species, the two species formed separate microcolonies. The structure development in the consortium was studied online using a gfp‐tagged Pseudomonas sp. B13(FR1) derivative. After a shift in carbon source from citrate to a low concentration of chlorobiphenyl, movement of the Pseudomonas sp. B13(FR1) bacteria led to a change in the spatial structure of the consortium from the unassociated form towards the associated form within a few days. Experiments involving a gfp‐based Pseudomonas sp. B13(FR1) growth activity reporter strain indicated that chlorobenzoate supporting growth of Pseudomonas sp. B13(FR1) is located close to the Burkholderia sp. LB400 microcolonies in chlorobiphenyl‐grown consortia.
Cadmium‐regulated gene fusions in Pseudomonas fluorescens
Authors: Rossbach Silvia , Kukuk Marsha L. , Wilson Thomas L. , Feng Szi Fei , Pearson Melanie M. , Fisher Marla A.
Published: March 2003

To study the mechanisms soil bacteria use to cope with elevated concentrations of heavy metals in the environment, a mutagenesis with the lacZ‐based reporter gene transposon Tn5‐B20 was performed. Random gene fusions in the genome of the common soil bacterium Pseudomonas fluorescens strain ATCC 13525 were used to create a bank of 5000 P. fluorescens mutants. This mutant bank was screened for differential gene expression in the presence of the toxic metal cadmium. Fourteen mutants were identified that responded with increased or reduced gene expression to the presence of cadmium. The mutants were characterized with respect to their metal‐dependent gene expression and their metal tolerance. Half the identified mutants reacted with differential gene expression specifically to the metal cadmium, whereas some of the other mutants also responded to elevated concentrations of copper and zinc ions. One of the mutants, strain C8, also showed increased gene expression in the presence of the solvent ethanol, but otherwise no overlap between cadmium‐induced gene expression and general stress response was detected. Molecular analysis of the corresponding genetic loci was performed using arbitrary polymerase chain reaction (PCR), DNA sequencing and comparison of the deduced protein products with sequences deposited in genetic databases. Some of the genetic loci targeted by the transposon did not show any similarities to any known genes; thus, they may represent ‘novel’ loci. The hypothesis that genes that are differentially expressed in the presence of heavy metals play a role in metal tolerance was verified for one of the mutants. This mutant, strain C11, was hypersensitive to cadmium and zinc ions. In mutant C11, the transposon had inserted into a genetic region displaying similarity to genes encoding the sensor/regulator protein pairs of two‐component systems that regulate gene expression in metal‐resistant bacteria, including czcRS of Ralstonia eutropha, czrRS of Pseudomonas aeruginosa and copRS of Pseudomonas syringae. Although the P. fluorescens strain used in this study had not been isolated from a metal‐rich environment, it nevertheless contained at least one genetic region enabling it to cope with elevated concentrations of heavy metals.
Detection of genes for alkane and naphthalene catabolism in Rhodococcus sp. strain 1BN
Authors: Andreoni Vincenza , Bernasconi Silvana , Colombo Milena , Van Beilen Jan B. , Cavalca Lucia
Published: March 2003

Rhodococcus sp. 1BN was isolated from a contaminated site and showed various biodegradative capabilities. Besides naphthalene, strain 1BN degraded medium‐ (C6) and long‐chain alkanes (C16–C28), benzene and toluene, alone or when the hydrocarbons were mixed in equal proportions. The nucleotide sequence of an alk polymerase chain reaction (PCR) fragment revealed a 59% nucleotide homology to the Pseudomonas oleovorans alkB gene. The nar fragments were highly homologous to genes coding for large and small subunits of cis‐naphthalene 1,2‐dioxygenase (narAa and narAb) and to cis‐naphthalene dihydrodiol dehydrogenase (narB) from other rhodococci. The oxidation of indene to cis‐(1S,2R)‐1,2‐dihydroxyindan by toluene‐induced cells allows to hypothesize that strain 1BN also carries a toluene dioxygenase‐like system.
Enhancing desulphurization by engineering a flavin reductase‐encoding gene cassette in recombinant biocatalysts
Authors: Galán Beatriz , Díaz Eduardo , García José L.
Published: March 2003

Biological desulphurization of petroleum feedstocks and products may offer an attractive alternative to reduce sulphur oxide emissions that cause serious environmental pollution. Dibenzothiophene (DBT) desulphurization via the Dsz pathway of Rhodococcus erythropolis IGTS8 is an energetically expensive process that consumes reducing equivalents. We have shown in this work that the HpaC oxidoreductase from Escherichia coli W is able to supply the required FMNH2 to the Dsz monooxygenases. The cloning and expression of the hpaC gene in Pseudomonas strains bearing the dszABC gene cluster significantly enhanced DBT desulphurization efficacy of the recombinant biocatalysts in a resting‐cell process, thus indicating that overexpression of a heterologous flavin reductase in the host cell is critical for a high rate of sulphur removal in vivo. The hpaC and dszABC genes have been engineered as a single transcription unit under control of broad‐host‐range regulatory signals in a mobilizable DNA cassette that can be used to confer a DBT desulphurization phenotype to a wide variety of bacteria regardless of the expression of putative housekeeping flavin reductases within the host cells. This cassette will be very useful in exploring the biotechnological potential of novel biocatalysts for developing an efficient desulphurization process.
Isolate PM1 populations are dominant and novel methyl tert‐butyl ether‐degrading bacteria in compost biofilter enrichments
Authors: Bruns Mary Ann , Hanson Jessica R. , Mefford Joel , Scow Kate M.
Published: March 2003

The gasoline additive MTBE, methyl tert‐butyl ether, is a widespread and persistent groundwater contaminant. MTBE undergoes rapid mineralization as the sole carbon and energy source of bacterial strain PM1, isolated from an enrichment culture of compost biofilter material. In this report, we describe the results of microbial community DNA profiling to assess the relative dominance of isolate PM1 and other bacterial strains cultured from the compost enrichment. Three polymerase chain reaction (PCR)‐based profiling approaches were evaluated: denaturing gradient gel electrophoresis (DGGE) analysis of 230 bp 16S rDNA fragments; thermal gradient gel electrophoresis (TGGE) analysis of 575 bp 16S rDNA fragments; and non‐denaturing polyacrylamide gel electrophoresis of 300–1500 bp fragments containing 16S/23S ribosomal intergenic transcribed spacer (ITS) regions. Whereas all three DNA profiling approaches indicated that PM1‐like bands predominated in mixtures from MTBE‐grown enrichments, ITS profiling provided the most abundant and specific sequence data to confirm strain PM1′s presence in the enrichment. Moreover, ITS profiling did not produce non‐specific PCR products that were observed with T/DGGE. A further advantage of ITS community profiling over other methods requiring restriction digestion (e.g. terminal restriction fragment length polymorphisms) was that it did not require an additional digestion step or the use of automated sequencing equipment. ITS bands, excised from similar locations in profiles of the enrichment and PM1 pure culture, were 99.9% identical across 750 16S rDNA positions and 100% identical across 691 spacer positions.

blast comparisons of nearly full‐length 16S rDNA sequences showed 96% similarity between isolate PM1 and representatives of at least four different genera in the Leptothrix subgroup of the β‐Proteobacteria (Aquabacterium, Leptothrix, Rubrivivax and Ideonella). Maximum likelihood and parsimony analyses of 1249 nucleotide positions supported isolate PM1′s position in a separate lineage within the Leptothrix subgroup.
Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus
Authors: Tor Jason M. , Lovley Derek R.
Published: March 2003

Aromatic compounds are an important component of the organic matter in some of the anaerobic environments that hyperthermophilic microorganisms inhabit, but the potential for hyperthermophilic microorganisms to metabolize aromatic compounds has not been described previously. In this study, aromatic metabolism was investigated in the hyperthermophile Ferroglobus placidus. F. placidus grew at 85°C in anaerobic medium with a variety of aromatic compounds as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. Growth coincided with Fe(III) reduction. Aromatic compounds supporting growth included benzoate, phenol, 4‐hydroxybenzoate, benzaldehyde, p‐hydroxybenzaldehyde and t‐cinnamic acid (3‐phenyl‐2‐propenoic acid). These aromatic compounds did not support growth when nitrate was provided as the electron acceptor, even though nitrate supports the growth of this organism with Fe(II) or H2 as the electron donor. The stoichiometry of benzoate and phenol uptake and Fe(III) reduction indicated that F. placidus completely oxidized these aromatic compounds to carbon dioxide, with Fe(III) serving as the sole electron acceptor. This is the first example of an Archaea that can anaerobically oxidize an aromatic compound. These results also demonstrate for the first time that hyperthermophilic microorganisms can anaerobically oxidize aromatic compounds and suggest that hyperthermophiles may metabolize aromatic compounds in hot environments such as the deep hot subsurface and in marine and terrestrial hydrothermal zones in which Fe(III) is available as an electron acceptor.
Transcript and activity levels of different Pleurotus ostreatus peroxidases are differentially affected by Mn2+
Authors: Cohen Roni , Hadar Yitzhak , Yarden Oded
Published: March 2003

The white‐rot fungus Pleurotus ostreatus produces both manganese‐dependent peroxidase (MnP) and versatile peroxidase (VP) in non‐manganese‐amended peptone medium (PM). We studied the effect of Mn2+ supplementation on MnPs and VPs in P. ostreatus by analysing the enzymatic and transcript abundance profiles of the peroxidases, as well as the lignin mineralization rate. The fungus was grown in PM under solid‐state conditions using perlite as an inert solid support. Mn2+ amendment resulted in a 1.7‐fold increase in [14C]‐lignin mineralization relative to unamended medium. Anion‐exchange chromatography was used to resolve the fungal peroxidase's enzymatic activity profile. Five peaks (P1–P5) of VP and one peak (P6) of MnP activity were detected in unamended medium. In Mn2+‐amended medium, a reduction in the activity of the VPs was observed. On the other hand, a sharp increase in the MnP activity level of peak P6 was detected. The P6 isoenzyme was purified and showed manganese‐dependent peroxidation of phenolic substrates. Internal sequence analysis of the purified enzyme revealed 100% identity with the deduced amino acid sequence of P. ostreatus MnP3 (GenBank AB016519). The effect of Mn2+ on the relative abundance of gene transcripts of three VPs and one MnP from P. ostreatus was monitored using reverse transcription–polymerase chain reaction (RT–PCR) with oligonucleotide primer sets synthesized on the basis of non‐conserved sequences of the different peroxidases. The reduction in VP gene transcript abundance and the increase in mnp3 transcript level were collinear with the changes observed in the enzyme activity profiles. These results indicate that the activity of peroxidases is regulated at the transcriptional level. We suggest that the expression of MnP and VP may be differentially regulated by the presence of Mn2+.
Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation
Authors: Courtois Sophie , Frostegård Åsa , Göransson Pernilla , Depret Geraldine , Jeannin Pascale , Simonet Pascal
Published: March 2003

All molecular analyses of soil bacterial diversity are based on the extraction of a representative fraction of cellular DNA. Methods of DNA extraction for this purpose are divided into two categories: those in which cells are lysed within the soil (direct extraction) and those in which cells are first removed from soil (cell extraction) and then lysed. The purpose of this study was to compare a method of direct extraction with a method in which cells were first separated from the soil matrix by Nycodenz gradient centrifugation in order to evaluate the effect of these different approaches on the analysis of the spectrum of diversity in a microbial community. We used a method based on polymerase chain reaction (PCR) amplification of a 16S rRNA gene fragment, followed by hybridization of the amplified fragments to a set of specific probes to assess the phylogenetic diversity of our samples. Control parameters, such as the relationship between amount of DNA template and amount of PCR product and the influence of competing DNA on PCR amplification, were first examined. Comparison between extraction methods showed that less DNA was extracted when cells were first separated from the soil matrix (0.4 µg g−1 dry weight soil versus 38–93 µg g−1 obtained by in situ lysis methods). However, with the exception of the γ‐subclass of Proteobacteria, there was no significant difference in the spectrum of diversity resulting from the two extraction strategies.
Distribution of S‐layers on the surface of Bacillus cereus strains: phylogenetic origin and ecological pressure
Authors: Mignot Tâm , Denis Benjamin , Couture‐Tosi Evelyne , Kolstø Anne‐Brit , Mock Michèle , Fouet Agnès
Published: March 2003

Bacillus anthracis, Bacillus cereus and Bacillus thuringiensis have been described as members of the Bacillus cereus group but are, in fact, one species. B. anthracis is a mammal pathogen, B. thuringiensis an entomopathogen and B. cereus a ubiquitous soil bacterium and an occasional human pathogen. In two clinical isolates of B. cereus, in some B. thuringiensis strains and in B. anthracis, an S‐layer has been described. We investigated how the S‐layer is distributed in B. cereus, and whether phylogeny or ecology could explain its presence on the surface of some but not all strains. We first developed a simple biochemical assay to test for the presence of the S‐layer. We then used the assay with 51 strains of known genetic relationship: 26 genetically diverse B. cereus and 25 non‐B. anthracis of the B. anthracis cluster. When present, the genetic organization of the S‐layer locus was analysed further. It was identical in B. cereus and B. anthracis. Nineteen strains harboured an S‐layer, 16 of which belonged to the B. anthracis cluster. All 19 were B. cereus clinical isolates or B. thuringiensis, except for one soil and one dairy strain. These findings suggest a common phylogenetic origin for the S‐layer at the surface of B. cereus strains and, presumably, ecological pressure on its maintenance.
Impact of ionic aluminium on extracellular phosphatases in acidified lakes
Authors: Bittl Thomas , Vrba Jaroslav , Nedoma Jiří , Kopáček Jiří
Published: March 2003

We studied direct inhibiting effects of aluminium (Al) on extracellular phosphatases produced by the plankton of acidified lakes in the Bohemian Forest. In laboratory experiments we tested the effect of different Al concentrations (0–1000 µg l−1) on kinetic parameters of acid phosphatases (pH optimum ∼5.0) at pH between 4.5 and 5.2. We observed a significant reduction of an apparent substrate affinity at Al concentrations between 300 and 1000 µg l−1 at pH 4.5 and 4.8 (but not at 5.2). In contrast, maximum acid phosphatase activity (AcPA) remained unchanged. Such behaviour of saturation kinetics is compatible with the assumption that ionic Al acts as a competitive inhibitor of acid phosphatases. To decide whether the observed Al effects could be explained alternatively by complexation of Al with substrate, we tested statistically the best fits of data with both possible models (competitive versus complexation). Experimental results supported the competitive hypothesis rather than the complexation model suggested originally by some authors. Furthermore, we tested the Al effect within a wide range of pH from 4.0 to 6.0. For pH values < 5.2, the results of an Al–pH matrix experiment gave a more detailed picture: the higher the Al concentration, the wider the pH range in which Al could negatively affect AcPA. The ecological ramifications of this effect were evaluated in the context of field AcPA data on three strongly acidified lakes.
Detection and activity of insertion sequences in environmental strains of Burkholderia
Authors: Miché Lucie , Faure Denis , Blot Michel , Cabanne‐Giuli Estelle , Balandreau Jacques
Published: March 2003

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 statistically significant correlation was found between the occurrences of IS406 and IS407. Moreover, PCR–RFLP studies of the amplified fragments showed that IS406 is largely conserved among all the strains tested, whereas IS407 is rather polymorphic. Transposition activity was studied in Burkholderia vietnamiensis TVV75, using the pGBG1 target plasmid. This entrapping plasmid permitted the isolation and characterization of three active IS, able to activate the plasmid‐borne tetA gene after transposition. Sequencing permitted the identification of these mobile genetic elements as isoforms of IS402, IS407 and IS1416. PCR amplification products provided IS probes, which were used to determine the copy‐numbers of IS402, IS407 and IS1416 in the genome of B. vietnamiensis TVV75, by Southern blotting. Copy numbers are 12, 3 and 11 respectively. To our knowledge, this is the first description of active insertion sequences in B. vietnamiensis.
Effects of two different application methods of Burkholderia ambifaria MCI 7 on plant growth and rhizospheric bacterial diversity
Authors: Ciccillo Fabio , Fiore Alessia , Bevivino Annamaria , Dalmastri Claudia , Tabacchioni Silvia , Chiarini Luigi
Published: March 2003

In order to acquire a better understanding of the effects of the different delivery modes of bacterial inoculants on plant growth and on the community structure of rhizosphere bacterial populations, Burkholderia ambifaria MCI 7 (formerly B. cepacia MCI 7) was inoculated into the rhizosphere of maize plants by either seed adhesion or incorporation into soil. Plant growth was evaluated at different inoculum concentrations. The community structure of rhizosphere bacterial populations was evaluated by analysing the restriction patterns of the DNA coding for 16S rRNA amplified by polymerase chain reaction (PCR) (ARDRA) of 745 bacterial isolates. A number of diversity indices (richness, Shannon diversity, evenness and mean genetic distance) were calculated for each bacterial population isolated from control and treated plants according to the concept of the r/K strategy. Moreover, the analysis of molecular variance (AMOVA) method was applied to estimate the genetic differences among the various bacterial populations. Our results showed that the method of application can be an essential element in determining the effects of the inoculant on plant growth. In fact, when applied as a maize seed treatment, B. ambifaria MCI 7 promoted plant growth significantly; on the contrary, when incorporated into soil, the same strain reduced plant growth markedly. As far as the bacterial community structure is concerned, B. ambifaria MCI 7 affected the indigenous microflora of treated plants according to the application method: seed treatment brought about an abrupt decrease in bacterial diversity, whereas incorporation into soil increased bacterial diversity. Moreover, changes in bacterial diversity were limited to r‐strategist bacteria. In conclusion, B. ambifaria MCI 7 can act as both a plant growth‐promoting rhizobacterium and a deleterious rhizobacterium depending on the inoculation method.
Analysis of sMMO‐containing Type I methanotrophs in Lake Washington sediment
Authors: Auman Ann J. , Lidstrom Mary E.
Published: March 2003

Methane‐oxidizing bacteria (methanotrophs) containing soluble methane monooxygenase (sMMO) are of interest in natural environments due to the high co‐metabolic activity of this enzyme with contaminants such as trichloroethylene. We have analysed sMMO‐containing methanotrophs in sediment from a freshwater lake. Environmental clone banks for a gene encoding a diagnostic sMMO subunit (mmoX) were generated using DNA extracted from Lake Washington sediment and subjected to RFLP analysis. Representatives from the six RFLP groups were cloned and sequenced, and all were found to group with Type I Methylomonas mmoX, although a majority were divergent from known Methylomonas mmoX sequences. Direct hybridization of Lake Washington sediment DNA was carried out using a series of sMMO‐ and Methylomonas‐specific probes to assess the significance of these sMMO‐containing Methylomonas‐like strains in the sediment. The total sMMO‐containing population and the sMMO‐containing Methylomonas‐like population were estimated to be similar to previous estimates for total methanotrophs and Type I methanotrophs. These results suggest that the major methanotrophic population in Lake Washington sediment consists of sMMO‐containing Methylomonas‐like (Type I) methanotrophs. The whole‐cell TCE degradation kinetics of such a strain, LW15, isolated from this environment, were determined and found to be similar to values reported for other sMMO‐containing methanotrophs. The numerical significance of sMMO‐containing Methylomonas‐like methanotrophs in a mesotrophic lake environment suggests that these methanotrophs may play an important role in methanotroph‐mediated transformations, including co‐metabolism of halogenated solvents, in natural environments.
Metabolic biomarkers for monitoring anaerobic naphthalene biodegradation in situ
Authors: Phelps Craig D. , Battistelli Joseph , Young L. Y.
Published: March 2003

During the anaerobic biodegradation of naphthalene and methylnaphthalene, unique metabolites are formed by specific microbial carboxylation and ring‐reduction reactions. Groundwater samples from an anoxic, shallow aquifer contaminated with gasoline were examined for the presence of these metabolites by extraction, derivatization and gas chromatography coupled to mass spectroscopy. Several metabolites [2‐naphthoic acid (2‐NA), tetrahydro‐2‐naphthoic acid (TH‐2‐NA), hexahydro‐2‐naphthoic acid (HH‐2‐NA) and methylnaphthoic acid (MNA)] were found to be present in the groundwater samples. The concentration of 2‐NA at each monitoring well was quantified and correlated to the zones of contamination. The presence of the other metabolites in the same wells as 2‐NA was used as confirmation that the anaerobic pathway was indeed active. The distribution of metabolites at this site shows that they can be used as biomarkers for demonstrating in situ biodegradation.
Extremely productive microbial communities in shallow saline pools respond immediately to changing meteorological conditions
Authors: Kirschner A. K. T. , Eiler A. , Zechmeister T. C. , Velimirov B. , Herzig A. , Mach R. , Farnleitner A. H.
Published: March 2003

Diel changes in bacterial and cyanobacterial numbers, as well as heterotrophic bacterial production, were examined in two shallow alkaline pools, harbouring dense populations of cyanobacteria (up to 1100 × 109 cells l−1) and bacteria (up to 500 × 109 cells l−1). Together with the recorded bacterial production rates (925 µgC l−1 h−1), these values are the highest reported for natural aquatic ecosystems. The investigations were performed during a fair‐weather situation, and during a rapid change after a long‐term fair‐weather situation to thunderstorms and heavy rainfall. During fair weather, bacterial growth was significantly correlated to the diurnal light and temperature cycle. Prokaryotic abundances were fairly constant, and loss by grazing and viral lysis must have been of significant importance. During the invasion of rainy weather, the prokaryotic community showed a strong and immediate response. A significant enhancement of bacterial growth followed after rainfall, suggesting that the high salt concentrations had inhibited bacterial activity. Changes in bacterial and cyanobacterial numbers were consistent with this pattern. From comparison with the available literature, we conclude that diel changes of bacterioplankton are regulated by a complex combination of environmental factors specific for each investigated ecosystem. In the soda pools investigated, external abiotic factors were dominant on a diel scale. In larger ecosystems, such factors are much more buffered and internal biotic interactions may prevail.
Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment
Authors: Toro Nicolás
Published: March 2003

Self‐splicing group II introns are present in the organelles of lower eukaryotes, plants and Bacteria and have been found recently in Archaea. It is generally accepted that group II introns originated in bacteria before spreading to mitochondria and chloroplasts. These introns are thought to be related to the progenitors of spliceosomal introns. Group II introns are also mobile genetic elements. In bacteria, they appear to spread using either other mobile genetic elements or low‐expression regions as target sites. Bacteria and Archaea genome sequence annotations have revealed the diversity of group II intron classes and that they are involved in vertical and horizontal inheritance.
Prolonged delay in healing after surgical treatment of pilonidal sinus is avoidable
Authors: Patel  , Lee  , Bloom  , Allen‐Mersh
Published: March 2003

A chronically infected sacral wound requiring repeated shaving, cleansing and dressing after treatment of pilonidal sinus disrupts both work and social activity.

Objective

To compare delay in pilonidal sinus wound healing after laying open with that after primary closure.

Patients and method

Healing time and recurrence were recorded in a consecutive series of 102 patients in one hospital undergoing either asymmetric primary closure (Karydakis procedure) by a single surgeon or laying open by other surgeons.

Results

The interval from operation to cessation of wound dressing was significantly shorter (log rank test, P < 0.0003) after primary closure (median 3 weeks, iqr 3–6) compared with laying open (median 6 weeks, iqr 4–8). No primary closure (0%) and 10 laid open (19%) wounds remained unhealed at 10 weeks from operation (2 × 2 contingency table, P = 0.003). No significant difference was demonstrated (Mann–Whitney U‐test) between healing time in elective (median 3 weeks, iqr 3–6) compared with emergency (median 3 weeks, iqr 3–3) admissions treated by primary closure.

Conclusions

Prolonged delay in healing after surgical treatment of pilonidal sinus is avoidable.
Follow up of more than 10 years after strictureplasty for jejunoileal Crohn’s disease: long‐term results and predictive factors for outcome
Authors: Yamamoto  , Keighley
Published: March 2003

Objective

The long‐term outcome of strictureplasty for Crohn’s disease is unknown. There have been few reports that have examined the predictive factors for outcome after strictureplasty. This study was undertaken to assess the long‐term results and predictive factors for outcome following strictureplasty for jejunoileal Crohn’s disease.

Patients and methods

Thirty‐eight patients who underwent primary strictureplasty for jejunoileal Crohn’s disease between 1980 and 1987 were reviewed.

Results

Four patients developed an enterocutaneous fistula, of whom two had an intra‐abdominal abscess. Two patients died during this study (one from leukaemia and another from small bowel carcinoma) and one patient was lost to follow up. All other patients have been followed for> 10 years. The 5‐ and 10‐year cumulative reoperation rates for recurrence at the previous jejunoileal strictureplasty sites (site‐specific recurrence) were 26% and 29%, respectively, after a median follow up of 13.5 years. After 5 years only one patient required surgery for site‐specific recurrence. The only factor associated with a high rate of reoperation for site‐specific recurrence was youth (<35 years). Gender, duration of symptoms, smoking habits, preoperative steroids therapy, preoperative albumin level, intra‐abdominal abscess at laparotomy, number or length of strictureplasties, or previous or synchronous small bowel resection did not affect the reoperation rate.

Conclusions

Strictureplasty is a safe and efficacious procedure for jejunoileal Crohn’s disease in the long term. Recurrence tends to develop early after strictureplasty, and late recurrence is uncommon. Only youth was a significant risk factor for site‐specific recurrence requiring reoperation.
Influence of peri‐operative immunotherapy on serum cytokines and soluble cytokine receptors in patients undergoing surgery for colorectal cancer
Authors: Nichols  , Ward  , Gallati  , Primrose
Published: March 2003

Objective

The cellular immune response is suppressed following surgery for colorectal cancer. As cytokines influence the patient’s immunological responsiveness, we have measured serum cytokines and their soluble receptors in patients receiving peri‐operative immunotherapy for colorectal cancer.

Patients and methods

Fifty‐two patients were randomized to receive low dose recombinant IL‐2 (rIL‐2) alone; rIL‐2 with interferon‐alpha (IFN‐α) or no immunotherapy. Serum cytokines and cytokine receptor levels were measured preoperatively and on post‐operative days 1, 4, 7 and 10 using ELISA kits.

Results

Circulating levels of IFN‐γ were undetectable in the majority of patients, although IFN‐γR levels were increased in all three groups on the first post‐operative day (P < 0.05). Similarly, IL‐2 was undetectable in most subjects and not enhanced by treatment. However, IL‐2R was significantly induced in all patients (P < 0.001), and these levels were higher in both treatment groups when compared with control (P < 0.005). Tumour necrosis factor‐alpha (TNF‐α) was universally undetectable, but the TNF‐R p55 and p75 subunits were induced in all patients (P < 0.005); and as with IL‐2R, this was greater in the treatment groups (P < 0.01). Finally, IL‐6 production was induced in all groups (P < 0.005), but this was only noted on day 1.

Conclusion

Soluble cytokine receptors are induced by surgery, and levels of IL‐2R and TNF‐R are enhanced by exogenous rIL‐2 and rIL‐2 with IFN‐α. This augmentation suggests increased immunocompetence associated with low dose peri‐operative immunotherapy.
A double‐blind randomized placebo‐controlled trial of oral indoramin to treat chronic anal fissure
Authors: Pitt J. , Dawson P. M. , Hallan R. I. , Boulos P. B.
Published: March 2003

Background

Indoramin is an α1‐adrenoceptor antagonist and has been shown to reduce anal resting pressure. Its therapeutic potential has not been explored. The aim of this study was to determine the outcome of treatment with oral indoramin on patients with chronic anal fissure in the setting of a double‐blind randomized placebo‐controlled trial.

Methods

Twenty‐three patients with chronic anal fissure were computer randomized to receive a 6‐week course of oral indoramin (20 mg) or placebo in identical capsules, twice daily and with bulk‐forming laxatives. Pain was assessed by a visual analogue scale from 0 to 10. Anal resting pressure, heart rate and blood pressure were recorded. Patients were reviewed 1 h after taking the capsule and at 2, 6 and 12 weeks thereafter.

Results

Fourteen patients were randomized to indoramin and 9 to placebo. Maximum anal resting pressure was reduced from a mean of 96.4 cm H2O (± 32) to 67.6 cm H2O (± 26), 1 h after indoramin (P=0.02) and there was no significant change after placebo. There were no significant changes in heart rate or blood pressure. Pain was reduced in the placebo group from a score of 4.9 to 2.0 after 6 weeks (P < 0.01) but not in the indoramin group. After 6 weeks, healing had occurred in one (7%) patient in the indoramin group and in 2 (22%) in the placebo group (P > 0.1). After 3 months, the chronic anal fissure in the indoramin group had recurred. The trial was terminated early because of poor healing rates.

Conclusion

An oral dose of indoramin (20 mg) administered twice daily reduced anal resting pressure by 30% compared with pretreatment levels but was ineffective in healing chronic anal fissures.
Administration of Lactobacillus plantarum 299v reduces side‐effects of external radiation on colon anastomotic healing in an experimental model
Authors: Liu Q. , Nobaek S. , Adawi D. , Mao Y. , Wang M. , Molin G. , Ekelund M. , Jeppsson B.
Published: March 2003

Objective

Preoperative radiotherapy of patients with rectal carcinoma is frequently used to reduce the incidence of local recurrence. However, the radiation therapy is associated with several complications, including diarrhea, retarded anastomotic healing and mucosal atrophy. Exogenous administration of lactobacilli has been demonstrated to be effective in stimulating intestinal mucosal growth and reduce mucosal inflammation. The objective of this study was to examine the effects of Lactobacillus plantarum 299v administration on external radiation injury in colon anastomotic healing at different time points.

Material and methods

Sprague‐Dawley rats were treated with Lb. plantarum 299v or saline as control and received external radiation of the lower abdomen (10 Gy/day) on day 3 and 7 of the experiment. After 4 days, a colonic resection with anastomosis was performed. Animals were sacrificed on 4th, 7th and 11th day postoperatively. Body weight, white blood cell (WBC) count, mucosal myeloperoxidase (MPO) activity, hydroxyproline, nucleotide, DNA and RNA content, colonic bacterial microflora, bacterial translocation and histology were evaluated.

Results

On the 4th postoperative day body weight, WBC and MPO decreased significantly after radiation. On the 7th postoperative day MPO decreased after radiation. In the two irradiated groups it decreased significantly in the Lb. plantarum group compared to the radiated group without treatment. Collagen concentration on the 7th postoperative day was significantly higher in Lb. plantarum group without radiation compared to the group with radiation without Lb. plantarum. On the 11th postoperative day MPO was significantly higher in irradiated rats without treatment compared to Lb. plantarum treatment. The collagen concentration increased significantly in the irradiated Lb. plantarum group compared to the other two groups.

Conclusion

The collagen content decreased and MPO activity increased significantly of the colonic anastomosis in irradiated rats without treatment compared to those treated with Lb. plantarum. It therefore seems that administration of Lactobacillus plantarum 299v reduces the intestinal injury and inflammation following external radiation and improves the colonic anastomotic healing.
Successful treatment of chronic anal fissure with diltiazem gel
Authors: DasGupta R. , Franklin I. , Pitt J. , Dawson P. M.
Published: March 2003

Objective

Diltiazem is a calcium channel blocker that has shown potential to heal chronic anal fissures. We have prospectively evaluated the treatment of patients with anal fissure with diltiazem gel (SLA Pharma, UK).

Patients and methods

All patients with chronic anal fissure from September 1999 to May 2000 were treated topically with 8 mg 2% diltiazem hydrochloride gel (equivalent to 2 cm of gel supplied by SLA Pharma) three times daily. The 23 patients (12 female), median age 45 (range 22–80) years had a 2–36 month (median 6 months) history of fissure. These were associated with a sentinel tag in 9 (39%) patients.

Results

The fissure healed in 11 (48%) of 23 patients, including 6 (75%) of 8 patients who previously failed to heal with GTN ointment. There were no recurrences at 3 months and no adverse effects. Of the 12 patients who did not respond to diltiazem, 4 have undergone sphincterotomy.

Conclusion

Diltiazem gel has a healing rate similar to that observed with GTN ointment but there were no adverse effects, the recurrence rate was lower, and diltiazem was effective in 75% of patients previously treated unsuccessfully with GTN ointment.
Factors affecting survival after palliative resection of colorectal carcinoma
Authors: Harris G. J. C. , Senagore A. J. , Lavery I. C. , Church J. M. , Fazio V. W.
Published: March 2003

Objective

To determine the factors affecting survival following palliative large bowel resection for colorectal adenocarcinoma.

Patients and method

From the Colorectal Cancer Database of a single institution patients who had a palliative resection of a colorectal cancer from 1980 to 1993 inclusive were identified. Survival curves were constructed using the Kaplan‐Meier method. Criteria studied were sex, age at operation, site of tumour, T, N and M status, tumour differentiation, involvement of tumour margins, tumour fixity and the presence or absence of peritoneal, liver or distant metastases. Multivariate analysis of factors was conducted using Cox proportional hazards analysis.

Results

Three hundred and seventy‐seven patients (232 men, 145 women, median age 64 years) fitted the above criteria. Operative mortality was 5.6%. Crude 6 month survival rate was 71.1% and median survival 10.5 months. Significant factors affecting survival on univariate analysis were – Age (<75 vs. >75 years) (P=0.019); T status (T1/T2 vs. T3/T4) (P=0.039); nodal status (N0 vs. N1/N2) (P=0.0059); distant metastases (P=0.039) or liver metastases (P=0.0058); tumour differentiation (poor vs. moderate/well differentiated) (P < 0.001); involved tumour margins (P < 0.001). Multivariate analysis found the following factors significant: age (P=0.02), liver metastases (P=0.05), distant metastases (P=0.044), T status (P=0.042), nodal status (P=0.0063), tumour differentiation (P < 0.001) and involvement of tumour margins (P < 0.001).

Conclusions

The data suggest that palliative resection of advanced colorectal carcinoma should be considered carefully in patients with advanced age, where distant metastases are present and in cases when primary tumours can not be completely resected. For the remaining patients, palliative resection may be accomplished with acceptable operative mortality and postoperative survival.