Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores.

Clostridium difficile is the leading cause of hospital acquired diarrhoea in industrialised countries. Under conditions that are not favourable for growth, the pathogen produces metabolically dormant endospores via asymmetric cell division. These are extremely resistant to both chemical and physical stress and provide the mechanism by which C. difficile can evade the potentially fatal consequences of exposure to heat, oxygen, alcohol, and certain disinfectants. Spores are the primary infective agent and must germinate to allow for vegetative cell growth and toxin production. While spore germination in Bacillus is well understood, little is known about C. difficile germination and outgrowth. Here we use genome-wide transcriptional analysis to elucidate the temporal gene expression patterns in C. difficile 630 endospore germination. We have optimized methods for large scale production and purification of spores. The germination characteristics of purified spores have been characterized and RNA extraction protocols have been optimized. Gene expression was highly dynamic during germination and outgrowth, and was found to involve a large number of genes. Using this genome-wide, microarray approach we have identified 511 genes that are significantly up- or down-regulated during C. difficile germination (p≤0.01). A number of functional groups of genes appeared to be co-regulated. These included transport, protein synthesis and secretion, motility and chemotaxis as well as cell wall biogenesis. These data give insight into how C. difficile re-establishes its metabolism, re-builds the basic structures of the vegetative cell and resumes growth

A fast ethanol assay to detect seed deterioration

The most common way to test seed quality is to use a simple and reliable but time- and space-consuming germination test. In this paper we present a fast and simple method to analyse cabbage seed deterioration by measuring ethanol production from partially imbibed seeds. The method uses a modified breath analyser and is simple compared to gas chromatographic or enzymatic procedures. A modified method using elevated temperatures (40°C instead of 20°C) shortened the assay time and improved its sensitivity. The analysis showed an inverse correlation between ethanol production and seed quality (e.g. the final percentages or speed of germination and the number of normal seedlings). The increase in ethanol production was observed when cabbage seeds were deteriorated by storage under ambient conditions or hot water treatments, both of which reduced the number of normal seedlings. Premature seeds produced more ethanol upon imbibition than mature seeds. Ethanol production occurred simultaneously with oxygen consumption, indicating that lack of oxygen is not the major trigger for ethanol production

Bacillus cereus responses to acid stress

Coping with acid environments is one of the prerequisites for the soil saprophytic and human pathogenic lifestyle of Bacillus cereus. This minireview highlights novel insights in the responses displayed by vegetative cells and germinating spores of B. cereus upon exposure to low pH as well as organic acids, including acetic acid, lactic acid and sorbic acid. Insights regarding the possible acid-inflicted damage, physiological responses and protective mechanisms have been compiled based on single cell fluorescence microscopy, flow cytometry and transcriptome analyses

Feasibility Study: Vertical Farm EDEN

Hundreds of millions of people around the world do not have access to sufficient food. With the global population continuing to increase, the global food output will need to drastically increase to meet demands. At the same time, the amount of land suitable for agriculture is finite, so it is not possibly to meet the growing demand by simply increasing the use of land. Thus, to be able to feed the entire global population, and continue to do so in the future, it will be necessary to drastically increase the food output per land area. One idea which has been recently discussed in the scientific community is called Vertical Farming (VF), which cultivates food crops on vertically stacked levels in (high-rise) buildings. The Vertical Farm, so it is said, would allow for more food production in a smaller area. Additionally, a Vertical Farm could be situated in any place (e.g. Taiga- or desert regions, cities), which would make it possible to reduce the amount of transportation needed to deliver the crops to the supermarkets. The technologies required for the Vertical Farm are well-known and already being used in conventional terrestrial greenhouses, as well as in the designs of bioregenerative Life Support Systems for space missions. However, the economic feasibility of the Vertical Farm, which will determine whether this concept will be developed or not, has not yet been adequately assessed. Through a Concurrent Engineering (CE) process, the DLR Institute for Space Systems (RY) in Bremen, aims to apply its know-how of Controlled Environment Agriculture (CEA) Technologies in space systems to provide valuable spin-off projects on Earth and to provide the first engineering study of a Vertical Farm to assess its economic feasibility

Impact of anaerobic digestion on organic matter quality in pig slurry

Changes in pig slurry organic matter (OM) during anaerobic digestion (AD) were studied in a reactor to characterize OM evolution through AD. OM maturity and stability were evaluated using different biological and physico-chemical methods. Germination and growth chamber experiments revealed a higher maturity of digested slurry (DS) than raw slurry (RS). Soil incubations showed that DS was more stable than RS with a C-mineralization of 12.0 g CO2-C 100 g1 Corg after 49 days as compared to 17.6 g CO2-C100 g1 Corg. Biochemical fractionation showed a relative increase in stable compounds such as hemicellulose-like and lignin-like molecules. Fourier-transform infrared spectroscopy showed some changes in the chemical structures of OM with a reduction in the aliphatic chain, lipid and polysaccharide levels. A comparison between the evolution of OM during AD and the first weeks of a composting process showed almost identical changes. Finally a theoretical method called Fictitious Atomic-group Separation was applied to the elemental compositions of RS and DS. DS was less humified than RS and presented the properties of a fulvic acid, indicating that the observed stability in DS was mainly due to the biodegradation of the most labile compound

Anaerobic digestion as a tool to eliminate animal parasites and weed seeds

Anaerobic digestion of residual materials from animals and crops offers an opportunity to simultaneously produce bioenergy and plant fertilizers at single farms and in farm communities where input substrate materials and resulting digested residues are shared among member farms. A surplus benefit from this praxis may be the suppressing of propagules from harmful biological pest like animal parasites, pathogens, and weed seeds. In the BIOCONCENS project (http://www.icrofs.dk/Sider/Forskning/foejoIII_bioconcens.html) batch experiments were performed, where survival of six species of weeds and the pigs large roundworm Ascaris suum (non-embryonated eggs) was assessed under conditions similar to biogas plants managed at meso- (37°C) and thermophilic (50°C) conditions. Cattle manure was used as digestion substrate and experimental units were sampled destructively during time. Regarding survival of A. suum, the effect of thermophilic conditions was highly significant as no eggs survived more than 3 h of incubation at 50°C. Incubation at 37°C did not affect egg survival during the first 48 h and it took up to 10 days before total elimination was reached. Similarly, at 50°C complete mortality of weed seeds, irrespective of species, was reached after less than two days. At mesophilic conditions, seeds of Avena fatua, Sinapsis arvensis, Solidago Canadensis had completely lost germination ability, while Brassica napus, Fallopia convolvulus and Amzinckia micranta still maintained low levels (~1%) of germination ability after one week. Chenopodium album was the only weed species which survived one week at substantial levels (7%) although after 11 d germination ability was totally lost. In general, anaerobic digestion in biogas plants seems an efficient way (thermophilic more efficient than mesophilic) to treat organic farm wastes in a way that suppresses animal parasites and weeds so that the digestates can be applied without risking the spread of these pests

Composting paper and grass clippings with anaerobically treated palm oil mill effluent

Purpose The purpose of this study is to investigate the composting performance of anaerobically treated palm oil mill effluent (AnPOME) mixed with paper and grass clippings. Methods Composting was conducted using a laboratory scale system for 40 days. Several parameters were determined: temperature, mass reduction, pH, electrical conductivity, colour, zeta potential, phytotoxicity and final compost nutrients. Results The moisture content and compost mass were reduced by 24 and 18 %, respectively. Both final compost pH value and electrical conductivity were found to increase in value. Colour (measured as PtCo) was not suitable as a maturity indicator. The negative zeta potential values decreased from −12.25 to −21.80 mV. The phytotoxicity of the compost mixture was found to decrease in value during the process and the final nutrient value of the compost indicates its suitability as a soil conditioner. Conclusions From this study, we conclude that the addition of paper and grass clippings can be a potential substrate to be composted with anaerobically treated palm oil mill effluent (AnPOME). The final compost produced is suitable for soil conditioner

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

Assessment of Biofertilizer Quality and Health Implications of Anaerobic Digestion Effluent of Cow Dung and Chicken Droppings

Anaerobic digestate have been identified as a rich source of essential plant nutrients. Nevertheless, its safety measured by the concentration of pathogen present is of great concern to end users. This research explored the efficiency of the mesophilic biodigestion process in the stabilization and sanitization of cow dung and chicken droppings. Six (6) kg each of cow dung and chicken droppings were collected fresh and free from impurities, pre-fermented, mixed with water in the ratio 1:1 w/v to form slurry, fed into the respective reactors and digested for 30 days at an average ambient temperature of 30 � 2 �C. The pH of the medium fluctuated between 6.5 and 8.0. The analysis of the feedstock and effluent of the digesters showed that a total solids reduction of 75.3% and 60.1% were recorded for cow dung and chicken droppings while the reduction in total coliforms was 95% and 70% respectively for the dung and droppings. Microbial analysis of the biofertilizer produced reveals both aerobic and anaerobic organisms which include species of Pseudomonas, Klebsiella, Clostridium, Bacillus, Bacteroides, Salmonella, Penicillum and Aspergillus. Escherichia coli and Shigella spp. were removed while species of Salmonella and Klebsiella were still present in the digestate. Notwithstanding these results, the digestate still requires further treatment for it to be suitable for application on unrestricted crops either as fertilizer; otherwise a health problem would be created as attempt is made to improve soil fertilit