Contrasting colonization and plant growth promoting capacity between wild type and a gfp-derative of the endophyte Pseudomonas putida W619 in hybrid poplar

This study aims to investigate the colonization of poplar by the endophyte Pseudomonas putida W619 and its capacity to promote plant growth. Poplar cuttings were inoculated with P. putida W619 (wild-type or gfp-labelled). The colonization of both strains was investigated and morphological, physiological and biochemical parameters were analyzed to evaluate plant growth promotion. Inoculation with P. putida W619 (wild-type) resulted in remarkable growth promotion, decreased activities of antioxidative defence related enzymes, and reduced stomatal resistance, all indicative of improved plant health and growth in comparison with the non-inoculated cuttings. In contrast, inoculation with gfp-labelled P. putida W619 did not promote growth; it even had a negative effect on plant health and growth. Furthermore, compared to the wildtype strain, colonization by the gfp-labelled P. putida W619::gfp1 was much lower; it only colonized the rhizosphere and root cortex while the wild-type strain also colonized the root xylem vessels. Despite the strong plant growth promoting capacity of P. putida W619 (wild-type), after gfp labelling its growth promoting characteristics disappeared and its colonization capacity was strongly influenced; for these reasons gfp labelling should be applied with sufficient caution.     

Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.     

Nitrogen in global animal production and management options for improving nitrogen use efficiency

Animal production systems convert plant protein into animal protein. Depending on animal species, ration and management, between 5% and 45 % of the nitrogen (N) in plant protein is converted to and deposited in animal protein. The other 55%-95% is excreted via urine and feces, and can be used as nutrient source for plant (= often animal feed) production. The estimated global amount of N voided by animals ranges between 80 and 130 Tg N per year, and is as large as or larger than the global annual N fertilizer consumption. Cattle (60%), sheep (12%) and pigs (6%) have the largest share in animal manure N production. The conversion of plant N into animal N is on average more efficient in poultry and pork production than in dairy production, which is higher than in beef and sheep production. However, differences within a type of animal production system can be as large as differences between types of animal production systems, due to large effects of the genetic potential of animals, animal feed and management. The management of animals and animal feed, together with the genetic potential of the animals, are key factors to a high efficiency of conversion of plant protein into animal protein. The efficiency of the conversion of N from animal manure, following application to land, into plant protein ranges between 0 and 60%, while the estimated global mean is about 15%. The other 40%-100% is lost to the wider environment via NH3 volatilization, denitrification, leaching and run-off in pastures or during storage and/or following application of the animal manure to land. On a global scale, only 40%-50% of the amount of N voided is collected in barns, stables and paddocks, and only half of this amount is recycled to crop land. The N losses from animal manure collected in barns, stables and paddocks depend on the animal manure management system. Relative large losses occur in confined animal feeding operations, as these often lack the land base to utilize the N from animal manure effectively. Losses will be relatively low when all manure are collected rapidly in water-tight and covered basins, and when they are subsequently applied to the land in proper amounts and at the proper time, and using the proper method (low-emission techniques). There is opportunity for improving the N conversion in animal production systems by improving the genetic production potential of the herd, the composition of the animal feed, and the management of the animal manure. Coupling of crop and animal production systems, at least at a regional scale, is one way to high N use efficiency in the whole system. Clustering of confined animal production systems with other intensive agricultural production systems on the basis of concepts from industrial ecology with manure processing is another possible way to improve N use efficiency.     

Evaluation of the Inheritance of the Complex Vertebral Malformation Syndrome by Breeding Studies

To investigate the congenital complex vertebral malformation syndrome (CVM) in Holstein calves, two breeding studies were performed including 262 and 363 cows, respectively. Cows were selected from the Danish Cattle Database based on pedigree and insemination records. Selected cows were progeny of sires with an established heterozygous CVM genotype and pregnant after insemination with semen from another sire with heterozygous CVM genotype. Following calving the breeders should state, if the calf was normal and was requested to submit dead calves for necropsy. In both studies, significantly fewer CVM affected calves than expected were obtained; a finding probably reflecting extensive intrauterine mortality in CVM affected foetuses. The findings illustrate increased intrauterine mortality as a major potential bias in observational studies of inherited disorders.     

Oestrone Sulphate Measurements for the Prediction of Small or Large Litters in Pigs

Serum from 88 pregnant sows and gilts was sampled 24 and 28 days after their first insemination or mating day. The oestrone sulphate (E1S) concentration in the samples was assessed with a commercially available radioimmunoassay kit modified for use with swine serum. The first aim was to test whether it was possible to predict litters of total number <10 piglets at term. The second aim was to compare the use of day 24 or day 28 samples, or of both, in this prediction.     

Microbial consortia that degrade 2,4-DNT by interspecies metabolism: isolation and characterisation

Two consortia, isolated by selective enrichment from a soil sample of anitroaromatic-contaminated site, degraded 2,4-DNT as their sole nitrogensource without accumulating one or more detectable intermediates. Thoughoriginating from the same sample, the optimised consortia had no commonmembers, indicating that selective enrichment resulted in different end points.Consortium 1 and consortium 2 contained four and six bacterial speciesrespectively, but both had two members that were able to collectivelydegrade 2,4-DNT. Variovorax paradoxus VM685 (consortium 1)and Pseudomonas sp. VM908 (consortium 2) initiate the catabolismof 2,4-DNT by an oxidation step, thereby releasing nitrite and forming4-methyl-5-nitrocatechol (4M5NC). Both strains contained a gene similarto the dntAa gene encoding 2,4-DNT dioxygenase. They subsequentlymetabolised 4M5NC to 2-hydroxy-5-methylquinone (2H5MQ) and nitrite,indicative of DntB or 4M5NC monooxygenase activity. A second consortiummember, Pseudomonas marginalis VM683 (consortium 1) and P.aeruginosa VM903, Sphingomonas sp. VM904, Stenotrophomonasmaltophilia VM905 or P. viridiflava VM907 (consortium 2), was foundto be indispensable for efficient growth of the consortia on 2,4-DNT and forefficient metabolisation of the intermediates 4M5NC and 2H5MQ. Knowledgeabout the interactions in this step of the degradation pathway is rather limited.In addition, both consortia can use 2,4-DNT as sole nitrogen and carbon source.A gene similar to the dntD gene of Burkholderia sp. strain DNT that catalyses ring fission was demonstrated by DNA hybridisation in the secondmember strains. To our knowledge, this is the first time that consortia are shownto be necessary for 2,4-DNT degradation.     

Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen

The effects of elevated atmospheric CO₂ (560 p.p.m.) and subsequent plant responses on the soil microbial community composition associated with trembling aspen was assessed through the classification of 6996 complete ribosomal DNA sequences amplified from the Rhinelander WI free-air CO₂ and O₃ enrichment (FACE) experiments microbial community metagenome. This in-depth comparative analysis provides an unprecedented, detailed and deep branching profile of population changes incurred as a response to this environmental perturbation. Total bacterial and eukaryotic abundance does not change; however, an increase in heterotrophic decomposers and ectomycorrhizal fungi is observed. Nitrate reducers of the domain bacteria and archaea, of the phylum Crenarchaea , potentially implicated in ammonium oxidation, significantly decreased with elevated CO₂. These changes in soil biota are evidence for altered interactions between trembling aspen and the microorganisms in its surrounding soil, and support the theory that greater plant detritus production under elevated CO₂ significantly alters soil microbial community composition.     

Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover

We present the full genome sequence of Clostridium sp. strain BNL1100, a Gram-positive, endospore-forming, lignocellulolytic bacterium isolated from a corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100 contains 4,025 putative protein-coding genes, of which 103 are glycoside hydrolases, the highest detected number in cluster III clostridia.     

Connective tissue growth factor is induced in bleomycin-induced skin scleroderma

The origin of fibrotic cells within connective tissue is unclear. For example, the extent to which microvascular pericytes contribute to the number of myofibroblasts present in dermal fibrosis in uncertain. Connective tissue growth factor (CTGF/CCN2) is a marker and mediator of fibrosis. In this report, we use an antibody recognizing CCN2 to assess the cell types in mouse dermis which express CCN2 in the bleomycin model of skin scleroderma. Control (PBS injected) and fibrotic (bleomycin-injected) dermis was examined for CCN2, α-smooth muscle actin (α-SMA) (to detect myofibroblasts), and NG2 (to detect pericytes) expression. Consistent with previously published data, CCN2 expression was largely absent in the dermis of control mice. However, upon exposure to bleomycin, CCN2 was observed in the dermis. Cells that expressed CCN2 were α−SMA-expressing myofibroblasts. Approximately 85% of myofibroblasts were NG2-positive, CCN2-expressing pericytes, indicating that pericytes significantly contributed to the presence of myofibroblasts in sclerotic dermis. Thus CCN2 is induced in fibrotic skin, correlating with the induction of myofibroblast induction. Moreover, CCN2-expressing pericytes significantly contribute to the appearance of myofibroblasts in bleomycin-induced skin scleroderma.     

Relationship between clinical signs and postmortem test status in cattle experimentally infected with the bovine spongiform encephalopathy agent

Background  

Various clinical protocols have been developed to aid in the clinical diagnosis of classical bovine spongiform encephalopathy (BSE), which is confirmed by postmortem examinations based on vacuolation and accumulation of disease-associated prion protein (PrP^d) in the brain. The present study investigated the occurrence and progression of sixty selected clinical signs and behaviour combinations in 513 experimentally exposed cattle subsequently categorised postmortem as confirmed or unconfirmed BSE cases. Appropriate undosed or saline inoculated controls were examined similarly and the data analysed to explore the possible occurrence of BSE-specific clinical expression in animals unconfirmed by postmortem examinations.