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PubMed1996

Fate of genetically modified Rhizobium leguminosarum biovar viciae during long-term storage of commercial inoculants.

A study was carried out to assess the behaviour, in terms of strain survival and genetic stability, of genetically modified micro-organisms (GEMs) during their storage in commercial-type agricultural inoculants. Three genetically modified Rhizobium leguminosarum biovar viciae strains were constructed, using a gene cassette containing an inducible lacZ gene from Escherichia coli and mercury resistance determinants from transposon Tn 1831. In the first case the genes have been integrated into the chromosome, the second strain contains the inducible cassette on a plasmid, in the third case the cassette is carried by the same plasmid, but the lacZ is constitutively expressed at high levels, due to the removal of the regulatory structure (lac operator) between the gene and its promoter. Three inoculum formulations, based on liquid, vermiculite and peat carriers, were prepared using the genetically modified strains, and were monitored during a period of up to 16 months. Results indicate a high stability of the chromosomally integrated markers. The plasmid-borne modification also was very stable, though the presence of the plasmid affected the strain growth kinetics. In contrast, the strain containing the highly expressed lacZ showed dramatic marker instability. Strain behaviour in stored inoculant packages reflected that observed in batch cultures; moreover, prolonged storage appeared to magnify differences found in in vitro cultures.

Cell Survival↗
PubMed2004

Comparison of application methods to prolong the survival of potential biocontrol bacteria on stored sugar-beet seed.

AIMS: To develop bacterial inoculation treatments on sugar-beet seed that will maintain a commercially acceptable degree of viability for a minimum of 4 months storage at ambient temperature. METHODS AND RESULTS: Single rifampicin-resistant (Rif(+)) strains of both Gram-positive and negative bacterial isolates (mostly pseudomonads) were applied in turn to sugar-beet seed in a comparative study by seed soaking, encapsulation in alginate, pelleting using an inoculated peat carrier or seed priming. The treated seed was assessed for bacterial survival over a time course by plating out homogenized samples onto a selective medium. Priming inoculation offered a significant improvement over all the other application strategies tested. After pelleting with fungicides and drying at 40 degrees C, Pseudomonas marginalis/putida P1W1 maintained populations of >6.6 log(10) CFU g(-1) seed during 4 months storage at 15 degrees C. Subsequent experiments verified a stabilized population under these storage conditions with commercial pellets at <7% moisture content. CONCLUSION: An inoculation method was established which allowed the survival on seed of a Gram-negative bacterium at ambient temperature with little loss in viability. SIGNIFICANCE AND IMPACT OF THE STUDY: This has promising implications for the delivery of beneficial bacteria, especially Gram-negative strains, on sugar beet.

Bacterial Physiological Phenomena↗
PubMed1989

Histamine control affects the weal produced by the adjacent diluent control in skin prick tests.

The effect of histamine chloride control (10 mg/ml) on the weal reaction produced by the adjacent test solution (buffered glycerol-saline diluent control) in skin prick tests was studied among 270 peat workers and 214 lumberjacks. The diluent control was placed on the skin at two test sites: 3-4 cm and 18-19 cm from the site of the histamine control. Prick-test lancets (Dome/Hollister-Stier) were used to prick the skin. Weal areas of 6 mm2 or larger were considered to be positive reactions. In both populations the diluent control caused positive reactions nearly three times more often when the test site was 3-4 cm from the site of the histamine control than when it was 18-19 cm away from the control (P less than 0.001). Similar relationships might be found between histamine control and allergen solutions. This finding should be taken into account in histamine-based standardisation of the results of skin prick tests as well as in biological standardization of allergen solutions.

Adult↗
PubMed2005

Methanogen communities and Bacteria along an ecohydrological gradient in a northern raised bog complex.

Mires forming an ecohydrological gradient from nutrient-rich, groundwater-fed mesotrophic and oligotrophic fens to a nutrient-poor ombrotrophic bog were studied by comparing potential methane (CH(4)) production and methanogenic microbial communities. Methane production was measured from different depths of anoxic peat and methanogen communities were detected by detailed restriction fragment length polymorphism (RFLP) analysis of clone libraries, sequencing and phylogenetic analysis. Potential CH(4) production changed along the ecohydrological gradient with the fens displaying much higher production than the ombrotrophic bog. Methanogen diversity also decreased along the gradient. The two fens had very similar diversity of methanogenic methyl-coenzyme M reductase gene (mcrA), but in the upper layer of the bog the methanogen diversity was strikingly lower, and only one type of mcrA sequence was retrieved. It was related to the Fen cluster, a group of novel methanogenic sequences found earlier in Finnish mires. Bacterial 16S rDNA sequences from the fens fell into at least nine phyla, but only four phyla were retrieved from the bog. The most common bacterial groups were Deltaproteobacteria, Verrucomicrobia and Acidobacteria.

Bacteria↗
PubMed2006

Design of Shewanella-specific 16S rRNA primers and application to analysis of Shewanella in a minerotrophic wetland.

In this study, an existing probe was used as a polymerase chain reaction (PCR) primer to study iron-reducing members of the genus Shewanella in a minerotrophic wetland where iron reduction had previously been implicated. The probe was found to be non-specific and a new set of PCR primers were developed that were specific for Shewanella. These primers were used to analyse the wetland iron-reducing communities by characterizing 16S rRNA genes amplified from DNA extracted from peat. Polymerase chain reaction clone libraries were screened using restriction fragment length polymorphism and diagnostic operational taxonomic units for Shewanella species were identified. A statistical method was used to determine the coverage of the clone libraries, which was found to be between 83% and 97%. The dominant species in the wetland samples at two geochemically distinct zones were phylogenetically related to the iron-reducing microorganism Shewanella oneidensis.

DNA Fingerprinting↗
PubMed1995

DIAMOND: a computerized system for the management and evaluation of district-wide diabetes care.

A computerized diabetic clinic management system, DIAMOND, has been developed with the collaboration of local general practitioners (GPs) to assist communication about diabetic patients across the district. DIAMOND is written in a Windows format using Microsoft Access and its dataset is in line with BDA and Diabcare recommendations. DIAMOND is user-friendly and includes displays and help messages throughout and does not require advanced computer knowledge. The main index contains two primary tables: a patient registration table with demographic data and an episode table with clinically important physical and biochemical measures. All entered data are coded to facilitate audit and an audit function, which automatically presents data, either numerically or graphically, is included in the report facility. DIAMOND also incorporates a system for patient education and training (PEATS) which may be operated by a health professional or the patient. Over 4500 patients in Newham are presently registered on DIAMOND with in excess of 15,000 episodes. Evaluation of this information is providing important clinical information both within individual GP practices and district-wide to assist future plans for health care provision.

Diabetes Mellitus↗
PubMed2006

Carbon balance of a European mountain bog at contrasting stages of regeneration.

Carbon dioxide and methane (CH4) fluxes were measured in a cutover bog of the Jura Mountains (France) together with biotic and abiotic variables for two entire vegetation periods in order to compare the carbon balance of the bog at three stages of regeneration. Among all factors, air temperature and vegetation index (including leaf area of vascular plants, bryophyte density and bryophyte desiccation) were the two main determinants of ecosystem respiration and gross photosynthesis at light saturation. During 2004 and 2005, the vegetated plots acted as carbon sinks. Net carbon exchange ranged between 67 and 166 g C m(-2) yr(-1) for the Eriophorum-dominated plots and between 93 and 183 g C m(-2) yr(-1) for the Sphagnum-dominated plots. The bare peat plots represented a net carbon source (between -19 and -32 g C m(-2) yr(-1)). Methane fluxes accounted for a very small part of the total carbon efflux (< 2%). The recovery of vegetation in our naturally regenerating bog was beneficial for the carbon sequestration after the relatively short period of 20 yr.

Carbon↗
PubMed2006

Contrasting phylogeographic patterns in Sphagnum fimbriatum and Sphagnum squarrosum (Bryophyta, Sphagnopsida) in Europe.

The chloroplast phylogeography of two peat mosses (Sphagnum fimbriatum and Sphagnum squarrosum) with similar distributions but different life history characteristics was investigated in Europe. Our main aim was to test whether similar distributions reflect similar phylogeographic and phylodemographic processes. Accessions covering the European distributions of the species were collected and approx. 2000 bp of the chloroplast genome of each species was sequenced. Maximum parsimony, statistical parsimony and phylodemographic analyses were used to address the question of whether these species with similar distributions show evidence of similar phylogeographic and phylodemographic processes. The chloroplast haplotypes of the currently spreading species S. fimbriatum showed strong geographic structure, whereas those of S. squarrosum, which has stable historical population sizes, showed only very weak geographic affinity and were widely distributed. We hypothesize that S. fimbriatum survived the last glaciations along the Atlantic coast of Europe, whereas S. squarrosum had numerous, scattered refugia in Europe. The dominance of one haplotype of S. fimbriatum across almost all of Europe suggests rapid colonization after the last glacial maximum. We hypothesize that high colonizing ability is an inherent characteristic of the species and its recent expansion in Europe is a response to climate change.

Biological Evolution↗
PubMed2004

Comparative analysis of Cryptosporidium, Giardia and indicator bacteria during sewage sludge hygienization in various composting processes.

AIMS: To evaluate the suitability of Clostridium perfringens, Escherichia coli and enterococci as indicator organisms for Cryptosporidium and Giardia in treated sludge. METHODS AND RESULTS: Occurrence of Cryptosporidium oocysts and Giardia cysts, detected and enumerated by direct immunofluorescence microscopy, were compared with counts of indicator bacteria during six different sewage sludge hygienization processes, including closed reactor and open windrow composting, and sludge sanitation by quicklime or peat addition. No statistical correlation existed between the counts of indicator bacteria, Cl. perfringens, E. coli, and enterococci and occurrence of Cryptosporidium or Giardia. In sludge end-products, Giardia cysts were detected more frequently than Cryptosporidium oocysts. SIGNIFICANCE OF THE STUDY: Direct analysis is the best method to confirm the presence of (oo)cysts in sludge.

Animals↗
PubMed2005

Phylloplane bacteria increase seedling emergence, growth and yield of field-grown groundnut (Arachis hypogaea L.).

AIM: To isolate and characterize groundnut-associated bacterial isolates for growth promotion of groundnut in field. METHODS AND RESULTS: Three hundred and ninety-three groundnut-associated bacteria, representing the geocarposphere, phylloplane and rhizosphere, and endophytes were applied as seed treatment in greenhouse. Maximum increase in plant biomass (up to 26%) was observed following treatment with a rhizosphere isolate identified as Bacillus firmis GRS 123, and two phylloplane isolates Bacillus megaterium GPS 55 and Pseudomonas aeruginosa GPS 21. There was no correlation between the production of L-tryptophan-derived auxins and growth promotion by the test isolates. Actively growing cells and peat formulations of GRS 123 and GPS 55, and actively growing cells of GPS 21, significantly increased the plant growth and pod yield (up to 19%) in field. Rifampicin-resistant mutants of GRS 123 and GPS 21 colonized the ecto- and endorhizospheres of groundnut, respectively, up to 100 days after sowing (DAS), whereas GPS 55 was recovered from both the habitats at 100 DAS. CONCLUSION: Seed bacterization with phylloplane isolates promoted groundnut growth indicating the possibility of isolating rhizosphere beneficial bacteria from different habitats. SIGNIFICANCE AND IMPACT OF THE STUDY: Identification of phylloplane bacteria as effective plant growth-promoting rhizobacteria (PGPR) broadens the spectrum of PGPR available for field application.

Anti-Bacterial Agents↗
PubMed2000

Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization(1).

We report here on novel groups of Archaea in the bacterioplankton of a small boreal forest lake studied by the culture-independent analysis of the 16S rRNA genes amplified directly from lake water in combination with fluorescent in situ hybridization (FISH). Polymerase chain reaction products were cloned and 28 of the 160 Archaea clones with around 900-bp-long 16S rRNA gene inserts, were sequenced. Phylogenetic analysis, including 642 Archaea sequences, confirmed that none of the freshwater clones were closely affiliated with known cultured Archaea. Twelve Archaea sequences from lake Valkea Kotinen (VAL) belonged to Group I of uncultivated Crenarchaeota and affiliated with environmental sequences from freshwater sediments, rice roots and soil as well as with sequences from an anaerobic digestor. Eight of the Crenarchaeota VAL clones formed a tight cluster. Sixteen sequences belonged to Euryarchaeota. Four of these formed a cluster together with environmental sequences from freshwater sediments and peat bogs within the order Methanomicrobiales. Five were affiliated with sequences from marine sediments situated close to marine Group II and three formed a novel cluster VAL III distantly related to the order Thermoplasmales. The remaining four clones formed a distinct clade within a phylogenetic radiation characterized by members of the orders Methanosarcinales and Methanomicrobiales on the same branch as rice cluster I, detected recently on rice roots and in anoxic bulk soil of flooded rice microcosms. FISH with specifically designed rRNA-targeted oligonucleotide probes revealed the presence of Methanomicrobiales in the studied lake. These observations indicate a new ecological niche for many novel 'non-extreme' environmental Archaea in the pelagic water of a boreal forest lake.

Journal Article↗
PubMed2006

Methanogen communities along a primary succession transect of mire ecosystems.

Peat accumulating mires are important sources of the greenhouse gas methane. Methane emissions and methanogenic Archaea communities have been shown to differ between fens and bogs, implying that mire succession includes an ecological succession in methanogen communities. We investigated methane production and the methanogen communities along a chronosequence of mires (ca. 100-2,500 years), which consisted of five sites (1-5) located on the land-uplift coast of the Gulf of Bothnia. Methane production was measured in a laboratory incubation experiment. Methanogen communities were determined by amplification of a methyl coenzyme M-reductase (mcr) gene marker and analyzed by terminal-restriction fragment length polymorphism. The terminal-restriction fragment length polymorphism fingerprinting resulted in 15 terminal restriction fragments. The ordination configuration of the terminal restriction fragments data, using nonmetric multidimensional scaling, showed a clear gradient in the methanogen community structure along the mire chronosequence. In addition, fingerprint patterns of samples from the water table level and 40 cm below differed from one another in the bog site (site 5). Methane production was negligible in the three youngest fen sites (sites 1-3) and showed the highest rates in the oligotrophic fen site (site 4). Successful PCR amplification using mcr gene primers revealed the presence of a methanogen community in all five sites along the study transect.

Biodiversity↗
PubMed1997

The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs.

The particulate methane monooxygenase gene pmoA, encoding the 27 kDa polypeptide of the membrane-bound particulate methane monooxygenase, was amplified by PCR from DNA isolated from a blanket peat bog and from enrichment cultures established, from the same environment, using methane as sole carbon and energy source. The resulting 525 bp PCR products were cloned and a representative number of clones were sequenced. Phylogenetic analysis of the derived amino acid sequences of the pmoA clones retrieved directly from environmental DNA samples revealed that they form a distinct cluster within representative PmoA sequences from type II methanotrophs and may originate from a novel group of acidophilic methanotrophs. The study also demonstrated the utility of the pmoA gene as a phylogenetic marker for identifying methanotroph-specific DNA sequences in the environment.

DNA Probes↗
PubMedDate not supplied

A first estimate of ground water ages for the deep aquifer of the Kathmandu Basin, Nepal, using the radioisotope chlorine-36.

The Kathmandu Basin in Nepal contains up to 550 m of Pliocene-Quaternary fluvio-lacustrine sediments which have formed a dual aquifer system. The unconfined sand and gravel aquifer is separated by a clay aquitard, up to 200 m thick, from the deeper, confined aquifer, comprised of Pliocene sand and gravel beds, intercalated with clay, peat, and lignite. The confined aquifer currently provides an important water supply to the central urban area but there are increasing concerns about its sustainability due to overexploitation. A limited number of determinations of the radioisotope 36Cl have been made on bore waters in the basin, allowing us to postulate on the age of ground water in the deeper, confined aquifer. Ground water evolution scenarios based on radioisotope decay, gradual dissolution of formational salts as the ground waters move downgradient, and flow velocity estimations produce comparable ground water ages for the deep waters, ranging from 200,000 to 400,000 years. From these ages, we deduce a mean ground water flow velocity of only 45 mm/year from recharge in the northeast to the main extraction region 15 km to the southwest. We thus estimate current recharge at about 5 to 15 mm/year, contributing 40,000 to 1.2 million m3/year to the ground water system. Current ground water extraction is estimated to be 20 times this amount. The low specific discharge confirms that the resource is being mined, and, based on current projections, reserves will be used up within 100 years.

Chlorine↗
PubMedDate not supplied

Heat as a tracer to estimate dissolved organic carbon flux from a restored wetland.

Heat was used as a natural tracer to characterize shallow ground water flow beneath a complex wetland system. Hydrogeologic data were combined with measured vertical temperature profiles to constrain a series of two-dimensional, transient simulations of ground water flow and heat transport using the model code SUTRA (Voss 1990). The measured seasonal temperature signal reached depths of 2.7 m beneath the pond. Hydraulic conductivity was varied in each of the layers in the model in a systematic manual calibration of the two-dimensional model to obtain the best fit to the measured temperature and hydraulic head. Results of a series of representative best-fit simulations represent a range in hydraulic conductivity values that had the best agreement between simulated and observed temperatures and that resulted in simulated pond seepage values within 1 order of magnitude of pond seepage estimated from the water budget. Resulting estimates of ground water discharge to an adjacent agricultural drainage ditch were used to estimate potential dissolved organic carbon (DOC) loads resulting from the restored wetland. Estimated DOC loads ranged from 45 to 1340 g C/(m2 year), which is higher than estimated DOC loads from surface water. In spite of the complexity in characterizing ground water flow in peat soils, using heat as a tracer provided a constrained estimate of subsurface flow from the pond to the agricultural drainage ditch.

Carbon↗
PubMed1983

Chronic obstructive pulmonary disease in the horse. 2: Therapy.

The therapy of equine chronic obstructive pulmonary disease (COPD) essentially entails minimising the horse's exposure to the aetiological antigens which are predominantly thermophilic actinomycetes and moulds occurring in hay and straw. This can be achieved, for example, by keeping affected horses permanently out of doors, or when stabled, using shredded paper, wood shavings or peat moss as bedding and feeding a complete cubed diet. There should be no supplementary hay feeding apart from dust-free vacuum-packed hay. Applying such measures generally allows horses to become asymptomatic in seven to 14 days. Bronchodilators and corticosteroids bring about a marked, but temporary, improvement and can be of value in the treatment of acute attacks. The use of oral bronchodilators in combination with environmental control measures may hasten the remission of clinical signs in affected horse. Inhaled sodium cromoglycate can be used prophylactically in asymptomatic horses to prevent the onset of COPD when unavoidable antigen exposure is anticipated.

Allergens↗
PubMed2025

Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).

Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. Despite intensive study, the extent to which hybridization is deterministic and repeatable, particularly in recurrent contact events involving the same species under varying ecological conditions, remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1300 individuals, we analysed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry, suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions and could be shaped by cytonuclear incompatibilities. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa, a morphologically distinct peat bog pine traditionally regarded as a relict and endangered species is instead a partially stabilised hybrid lineage. Its genome reflects incomplete hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognised as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.

Hybridization, Genetic↗
PubMed2003

Europe's terrestrial biosphere absorbs 7 to 12% of European anthropogenic CO2 emissions.

Most inverse atmospheric models report considerable uptake of carbon dioxide in Europe's terrestrial biosphere. In contrast, carbon stocks in terrestrial ecosystems increase at a much smaller rate, with carbon gains in forests and grassland soils almost being offset by carbon losses from cropland and peat soils. Accounting for non-carbon dioxide carbon transfers that are not detected by the atmospheric models and for carbon dioxide fluxes bypassing the ecosystem carbon stocks considerably reduces the gap between the small carbon-stock changes and the larger carbon dioxide uptake estimated by atmospheric models. The remaining difference could be because of missing components in the stock-change approach, as well as the large uncertainty in both methods. With the use of the corrected atmosphere- and land-based estimates as a dual constraint, we estimate a net carbon sink between 135 and 205 teragrams per year in Europe's terrestrial biosphere, the equivalent of 7 to 12% of the 1995 anthropogenic carbon emissions.

Agriculture↗