Characterization of a mobile and multiple resistance plasmid isolated from swine manure and its detection in soil after manure application
Published in Journal of Applied Microbiology, 26 April 2012
Aims: To isolate and characterize multiple antibiotic resistance plasmids found in swine manure and test for... more
Aims: To isolate and characterize multiple antibiotic resistance plasmids found in swine manure and test for plasmid-associated genetic markers in soil following manure application to an agricultural field.
Methods and Results: Plasmids were isolated from an erythromycin enrichment culture that used liquid swine manure as an inoculant. Plasmids were transformed into Escherichia coli DH10β for subsequent characterization. We isolated and DNA sequenced a 22 102-bp plasmid (pMC2) that confers macrolide, and tetracycline resistances, and carries genes predicted to code for mercury and chromium resistance. Conjugation experiments using an pRP4 derivative as a helper plasmid confirm that pMC2 has a functional mobilization unit. PCR was used to detect genetic elements found on pMC2 in DNA extracted from manure amended soil.
Conclusions: The pMC2 plasmid has a tetracycline-resistant core and has acquired additional resistance genes by insertion of an accessory region (12 762 bp) containing macrolide, mercury and chromium resistance genes, which was inserted between the truncated DDE motifs within the Tn903/IS102 mobile element.
Significance and Impact of the Study: Liquid swine manure used for manure spreading contains multiple antibiotic resistance plasmids that can be detected in soil following manure application.
Crystal Structure of ChrR - A Quinone Reductase with the Capacity to Reduce Chromate
PLoS ONE, 2012
Eswaramoorthy S and Poulain S (equal contributors), Hienerwadel R, Brémond N, Sylvester MD, Zhang Y-B, Berthomieu C, Van Der Lelie D, Matin A.
The Escherichia coli ChrR enzyme is an obligatory two-electron quinone reductase that has many applications, such as... more The Escherichia coli ChrR enzyme is an obligatory two-electron quinone reductase that has many applications, such as in chromate bioremediation. Its crystal structure, solved at 2.2 Å resolution, shows that it belongs to the flavodoxin superfamily in which flavin mononucleotide (FMN) is firmly anchored to the protein. ChrR crystallized as a tetramer, and size exclusion chromatography showed that this is the oligomeric form that catalyzes chromate reduction. Within the tetramer, the dimers interact by a pair of two hydrogen bond networks, each involving Tyr128 and Glu146 of one dimer and Arg125 and Tyr85 of the other; the latter extends to one of the redox FMN cofactors. Changes in each of these amino acids enhanced chromate reductase activity of the enzyme, showing that this network is centrally involved in chromate reduction.
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Seen by:Silver nanoparticles; size, function and areas for advancement
In press Advances in Applied Microbiology
Nanoparticles (NP) are attracting increased attention in commerce and applied microbiology due to their anti-microbial... more Nanoparticles (NP) are attracting increased attention in commerce and applied microbiology due to their anti-microbial activity, high electrical conductivity, and optical properties. For example, silver NPs have broad spectrum antimicrobial properties against a wide range of bacteria and fungi, making them ideal for minimizing biofouling. By controlling the size, shape, surface and agglomeration state of the NPs, specific ion release profiles can be developed for any given application. Currently NPs are formed in a wide variety of different shapes and sizes including spheres, plates and wires. This review will look at both commercially and naturally produced NP with a focus on silver NPs and address how these are formed. Furthermore potential areas for improving these techniques will be highlighted, focusing on advancing shape and structure formation using modern applications. Finally the review evaluates the feasibility of bioengineering microorganisms to synthesise particles of defined shape and size, by examining genes associated with NP production.
Bacterial assemblages differ between compartments within the coral holobiont
It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are... more It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the ‘snot sucker’) was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the ‘snot sucker’ and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.
Temporal and spatial patterns in waterborne bacterial communities of an island reef system
The bacterial 16S rRNA gene diversity of waterborne bacterial (WBB) communities was assessed using PCR/DGGE... more The bacterial 16S rRNA gene diversity of waterborne bacterial (WBB) communities was assessed using PCR/DGGE techniques, along with sequence analysis of selected bands. 16S rRNA gene diversity varied between seasons and significant differences were recorded between night and day. However, there were no significant differences detected between low, ebb, flood and high tides when the water body sampled would have originated from completely different areas including those off-reef. These results suggest that changes in productivity and/or vertical diurnal migrations of plankton may have greater effects than large scale water movements effected by tidal flows. These results do not demonstrate a strong link between WBB communities and their underlying benthos. This either suggests a lack of coupling between the benthos and the water column (benthic-pelagic coupling) or that the processes are extremely rapid and efficient with strong mixing. Previous studies at this site have shown cycling between coral reef and lagoon sediments via coral mucus release and tidal transport, supporting the latter. We found a strong seasonality in the abundance and composition of WBB communities, with α-proteobacteria being more prevalent during winter and γ-proteobacteria during summer but quantitative PCR (qPCR) showed no significant differences in vibrios between seasons.
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Seen by:Dynamics of bacterial community development in the reef coral Acropora muricata following experimental antibiotic treatment
Development of the bacterial community associated with the coral Acropora muricata (=formosa) was monitored using 16S... more Development of the bacterial community associated with the coral Acropora muricata (=formosa) was monitored using 16S rRNA gene-based techniques and abundance counts over time following experimental modification of the existing microbial community using the antibiotic ciprofloxacin. Abundance of bacteria was reduced >99% by the treatment, resulting in significant changes in bacterial community structure. Following redeployment to their natural environment, some settlement and re-growth of bacteria took place within a few hours, including ribosomal types that were not present, or in low abundance, in the natural microbiota. However, complete recovery of the bacterial community required longer than 96 h, which indicates a relatively slow settlement and growth of bacteria from the water column and suggests that turnover of the natural community is similarly slow. The early developing community was dominated by antibiotic-resistant bacteria from the natural microbiota that survived the treatment and proliferated in the absence of natural competitors, but also included some non-resident ribotypes colonizing from the water column. Almost, all these opportunists were significantly reduced or eliminated within 96 h after treatment, demonstrating a high resilience in the natural bacterial community. Potential pathogens, including a Clostridium sp., inhabited the coral at low abundances, only becoming prevalent when the natural microbiota was disturbed by the treatment. The healthy coral-associated microbiota appears to be strongly controlled by microbial interactions.
Ciliate and bacterial communities associated with White Syndrome and Brown Band Disease in reef building corals.
White Syndrome (WS) and Brown Band Disease (BrB) are important causes of reef coral mortality for which causal agents... more White Syndrome (WS) and Brown Band Disease (BrB) are important causes of reef coral mortality for which causal agents have not been definitively identified. Here we use culture-independent molecular techniques (DGGE and clone libraries) to characterise ciliate and bacterial communities in these diseases. Bacterial (16S rRNA gene) and ciliate (18S rRNA gene) communities were highly similar between the two diseases. Four bacterial and nine ciliate ribotypes were observed in both diseases, but absent in non diseased specimens. Only one of the bacteria, Arcobacter sp. (JF831360) increased substantially in relative 16S rRNA gene abundance and was consistently represented in all diseased samples. Four of the eleven ciliate morphotypes detected contained coral algal symbionts, indicative of the ingestion of coral tissues. In both WS and BrB, there were two ciliate morphotypes consistently represented in all disease lesion samples. Morph1 (JN626268) was observed to burrow into and underneath the coral tissues at the lesion boundary. Morph2 (JN626269), previously identified in BrB, appears to play a secondary, less invasive role in pathogenesis, but has a higher population density in BrB, giving rise to the visible brown band. The strong similarity in bacterial and ciliate community composition of these diseases suggests that they are actually the same syndrome.
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Coral diseases in aquaria and in nature
Many reef coral diseases have been described affecting corals in the wild, several of which have been associated with... more Many reef coral diseases have been described affecting corals in the wild, several of which have been associated with causal agents based on experimental inoculation and testing of Koch's postulates. In the aquarium industry, many coral diseases and pathologies are known from the grey literature but as yet these have not been systematically described and the relationship to known diseases in the wild is difficult to determine. There is therefore scope to aid the maintenance and husbandry of corals in aquaria by informing the field of the scientifically described wild diseases, if these can be reliably related. Conversely, since the main driver to identifying coral diseases in aquaria is to select an effective treatment, the lessons learnt by aquarists on which treatments work with particular syndromes provides invaluable evidence for determining the causal agents. Such treatments are not commonly sought by scientists working in the natural environment due the cost and potential environmental impacts of the treatments. Here we review both wild and aquarium diseases and attempt to relate the two. Many important aquarium diseases could not be reconciled to those in the wild. In one case, however, namely that of the ciliate Helicostoma sp. as a causal agent of brown jelly syndrome in aquarium corals, there may be similarities with pathogenic agents of the wild coral diseases, such as white syndrome and brown band syndrome. We propose that Helicostoma is actually a misnomer, but improved understanding of this pathogen and others could benefit both fields. Improved practices in aquarium maintenance and husbandry would also benefit natural environments by reducing the scale of wild harvest and improving the potential for coral culture, both for the aquarium industry and for rehabilitation programmes.
Silver Nanoparticles: A Microbial Perspective
Advances in Applied Microbiology
Silver nanoparticles (NPs) are used for a wide range of commercial reasons to restrict microbial growth. The... more Silver nanoparticles (NPs) are used for a wide range of commercial reasons to restrict microbial growth. The increasing use of silver NPs in modern materials ensures they will find their way into environmental systems. The mode of action which makes them desirable as an antimicrobial tool could also pose a severe threat to the natural microbial balance existing in these systems. Research into the potential environmental threats of silver NPs has mainly focused on particular areas, such as their influence in rivers and estuaries or their effect on organisms such as earthworms and plants. There is a need to focus studies on all aspects of the microbial world and to highlight potential risks and methods of overcoming problems before significant damage is done. This review focuses on the antimicrobial uses, mechanisms of toxicity, and effects on the environment (mainly soil) of silver NPs, illustrating gaps in current knowledge.
Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa
Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental... more Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. Accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. To investigate the effect of nutrition, perithecial development of Neurospora crassa was induced on two different media, a chemically sparsely nutritive Synthetic Crossing Medium (SCM) and a natural Carrot Agar (CA). Protoperithecia were collected before crossing, and perithecia were collected at 2, 24, 48, 72, 96, 120, and at full maturity 144h after crossing. No differences in fruiting body morphology were observed between the two media at any time point. A circuit of microarray hybridizations comparing cDNA from all neighboring stages was performed. For a majority of differentially expressed genes, expression was higher in SCM than in CA, and expression of core metabolic genes was particularly affected. Effects of nutrition were highest in magnitude before crossing, lowering in magnitude during early perithecial development. Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. However, for genes with key regulatory roles in sexual development, including pheromone precursor ccg-4 and poi2, expression patterns were similar between treatments. When possible, a common nutritional environment is ideal for comparing transcriptional profiles between different fungi. Nevertheless, the observed consistency of the developmental program across media, despite considerable metabolic differentiation is reassuring. This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi.
Investigation of Shelf Life of Potency and Activity of the Lactobacilli Produced Bacteriocins Through Their Exposure to Various Physicochemical Stress Factors
published in Probiotics and Antimicrobial Proteins
2012, DOI: 10.1007/s12602-012-9102-2 by Springer
Three Lactobacilli strains, Lactobacillus casei NCIMB 11970, Lactobacillus plantarum NCIMB 8014, Lactobacillus lactis... more Three Lactobacilli strains, Lactobacillus casei NCIMB 11970, Lactobacillus plantarum NCIMB 8014, Lactobacillus lactis NCIMB 8586 have been used for the production of bacteriocins. Though, their production phase, their biochemical nature, their mode of activity even their genetic structure have been widely investigated, there are hardly any studies investigating their potency and activity in depth of time, in other words their shelf life under several physicochemical conditions that may occur during their production in large scale. As such, the effect of several factors influencing the activity and the potency of bacteriocins when produced in large scale was examined as due to bacteriocins peptide nature degradation or denaturation might occur, under extreme physicochemical conditions. During scale-up process, differences between the output data may occur, such as concerning biomass, metabolic by-products and limiting substrate concentrations. These may affect negatively the activity and the potency of the bacteriocins. For investigating these effects and minimizing them, numerous studies were conducted, which were related to the exact phase of the production of these substances, the effect of dilution and temperature changes. These studies could be used in order to minimize the scaling-up effect when decided to produce these peptides in large scale.
Effects of reed straw, zeolite, and superphosphate amendments on NH3 and greenhouse gas emissions from stored duck manure
by Paul Kardol
J. Z.Wang, Z. Y. Hu, X. Q. Zhou, Z. Z. An, J. F. Gao, X. N. Liu, L. L. Jiang, J. Lu, X. M. Kang, M. Li, Y. B. Hao, P. Kardol. Journal of Environmental Quality, doi:10.2135/jeq2011.0373
Stored poultry manure can be a significant source of ammonia(NH3), and greenhouse gases (GHG), including nitrous... more Stored poultry manure can be a significant source of ammonia(NH3), and greenhouse gases (GHG), including nitrous oxide(N2O), methane (CH4), and carbon dioxide (CO2) emissions. Amendments can be utilized to modify physiochemical properties of manure, thus having the potential to reduce gas emissions. Here, we lab-tested the single and combined effects of addition of reed straw (S), zeolite (Z), and superphosphate (P) on gas emissions from stored duck manure. We showed that over a period of 46 days, cumulative NH3 emissions were reduced by 61-70% with superphosphate additions, while cumulative N2O emissions were increased by up to 23% compared with the control treatment. Reed straw addition reduced cumulative NH3, N2O, and CH4 emissions relative to the control by 12%, 27%, and 47%, respectively, while zeolite addition reduced cumulative NH3 and N2O emissions by 36% and 20%, respectively. Total GHG emissions (as CO2-equivalents) were reduced by up to 27% with the additions of reed straw and/or zeolite. Our results indicate that reed straw or zeolite can be recommended as amendments to reduce GHG emissions from duck manure; however, superphosphate is more effective in reducing NH3 emissions.
Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134
by Pere Puigbò
González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, Jaenicke S, Gómez-Consarnau L, Fernàndez-Guerra A, Goesmann A, Pedrós-Alió C.
Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine... more Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle.
Hydro-environmental modelling for bathing water compliance of an estuarine basin
by Roger Falconer - Cardiff University
Paper 64: Kashefipour, S. M., Lin, B., Harris, E. L. and Falconer, R. A. 2002. Hydro-environmental modelling for bathing water compliance of an estuarine basin. Water Research. 36(7), 1854-1868.
Abstract
In recent years, considerable investment has been committed to sewerage infrastructure and new sewage... more
Abstract
In recent years, considerable investment has been committed to sewerage infrastructure and new sewage treatment plants in the catchment surrounding an estuarine basin along the north-west coast of England. Although this capital investment has resulted in a marked reduction in the input of bacterial loads, relatively high counts of faecal indicator organisms are still being encountered in the coastal receiving waters, and the local bathing waters continue to fail on occasions to comply with the European Community (EC) Bathing Water Directive (1976) mandatory standards. Details are given herein of a comprehensive modelling study aimed at quantifying the impact of various bacterial inputs into the estuary and surrounding coastal waters on the bathing water quality. The model domain includes the coastal area and the entire estuary (namely the Ribble) up to the tidal limits of its tributaries. Faecal coliforms have been used as the main water quality indicator organisms. The numerical model developed for this study combines a depth integrated two-dimensional coastal model and a cross-sectionally integrated one-dimensional river model, and is capable of predicting water surface elevations, velocity fields and faecal coliform concentration distributions across the entire model domain. The hydrodynamic model was calibrated using water level and velocity measurements from three surveys and then validated against measured data from three other surveys. In order to predict the faecal coliform concentration distributions, variable faecal coliform decay rates were used, i.e. different values of decay rates were applied to the coastal and riverine waters, for day- and nighttime, and for wet and dry weather conditions. The maximum and minimum decay rates used were 2.32/day and 0.71/day for the dry and wet weather surveys, respectively. The model was then applied to (i) assess the impact of previous discharge strategies and investigate the effectiveness of future capital investment works and (ii) predict the impact of a range of strategic options, including: the effects of adding UV treatment, constructing storm water storage tanks and incorporating various combined sewer overflow (CSO) discharge scenarios for different weather conditions.
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Seen by:Development of a modelling tool to quantify faecal indicator levels in Cardiff Bay
by Roger Falconer - Cardiff University
Paper 65: Harris, E. L., Falconer, R. A., Kay, D. and Stapleton, C. 2002. Development of a modelling tool to quantify faecal indicator levels in Cardiff Bay. Proceedings of the Institution of Civil Engineers, Water and Maritime Engineering. 154(WME2), 129-135.
Abstract
The growing trend towards urban regeneration, particularly around water bodies, has made it... more
Abstract
The growing trend towards urban regeneration, particularly around water bodies, has made it increasingly important to predict the quality of urban waters. Furthermore, concern regarding hydro-environmental pollution has resulted in a marked increase in the development of computer models to assist in environmental impact assessment studies. Details are given of models used for flow and water quality indicator predictions in coastal and inland hydraulic basins, together with the limitations and restrictions of both physical and numerical models. Such models are now used routinely by non-specialist engineers and scientists to assist in the planning and design of water quality related studies. The paper then goes on to describe the development and application of a refined three-dimensional layer-integrated hydro-environmental model to predict water elevations, layer-averaged velocity components and the distribution of water quality indicators within Cardiff Bay, Wales. The model includes the prediction of flushing through the bay of spillages from combined sewer overflows or riverine inputs. Details are also given of field measurements taken for a range of variables used to describe the role of environmental factors and the interaction of various parameters in predicting the survival rates of bacteria in the numerical model.
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Seen by:Assessing factors underlying variation of CO2 emissions in boreal lakes versus reservoirs.
by Jérôme Marty
Reservoirs and lakes were compared to test the hypothesis that they are similar with respect to factors driving the... more
Reservoirs and lakes were compared to test the hypothesis that they are similar with respect to factors driving the variation in CO2 emissions to the atmosphere. Understanding this variation is necessary for the assessment of the contribution of these freshwater ecosystems to the global carbon cycle. This
study, in contrast to previous ones, included analyses of the relationships between CO2 emissions and microbial communities. Pooled data (lakes and reservoirs) showed that variations in CO2 emissions were strongly related to variations in temperature, dissolved organic matter (DOM) quality, and bacterial
production (BP). Results also showed that lakes were characterized by higher water temperature, lower DOM quality, larger size of Daphnia, and enriched d13C zooplankton compared to reservoirs. Moreover, interactions within plankton communities and relationships between CO2 emissions and zooplankton d13C signatures differed in lakes vs. reservoirs, indicating amongsystem
type differences in food web structure and carbon cycling. As a result of these ecosystem-type characteristics, CO2 emission variation was mainly explained by temperature and BP in lakes, and by DOM quality and the ratio of phytoplankton biomass to microheterotroph biomass in reservoirs. These results showed that differences in temperature and DOM quality between lakes
and reservoirs translate into differences in microbial interactions and ultimately in the importance of factors driving CO2 emissions to the atmosphere. They indicated that considering microbial communities and environmental variables such as temperature and DOM quality can help improve our understanding of the variation in CO2 emissions from freshwater ecosystems.
Comparative Study of Antibacterial Activity Of Garlic And Cinnamon At Different Temperature And Its Application On Preservation Of Fish
Co-Authored with- Nandita Dasgupta, Proud Saha, Madhumita Rakshit, C.Ramalingam.
Journal Name- Advances in Applied Science Research
The antibacterial effect of aqueous garlic and cinnamon extract at five different temperatures (40° C, 60°C, 80° C,... more The antibacterial effect of aqueous garlic and cinnamon extract at five different temperatures (40° C, 60°C, 80° C, 100° C, 120° C) against five multidrug resistant bacterial isolates (2 gram negative and 3 gram positive), including Bacillus cereus, Staphylococcus aureus, Enterococcus faecalis, E. Coli and Proteus mirabilis were studied by well diffusion method. The maximum antibacterial effect of aqueous garlic and cinnamon extract of different temperature obtained in Enterococcus faecalis and E. Coli at 60° C (1.041) and in Enterococcus faecalis at 60° C (0.87) respectively. This antibacterial property was applied on preservation of fish. A time dependent antibacterial study was done using the gum acacia coating with garlic and cinnamon paste. It is observed that the microbial load present on the fish was totally reduced on second day. In short, the aqueous garlic and cinnamon extract and pastes show a wide range of antibacterial activity at 40° C to 60° C and satisfy all the criteria for antibacterial agent as compared to antibiotic Gentamicin. These results suggests that garlic and cinnamon can be used as food preservative and thus the use of other chemical preservatives can be minimized, which would be beneficial for environment and consumer health; or a plastic for food preservation can be invented using the antibacterial activity of garlic and cinnamon, the inner wall of the plastic coated with garlic and cinnamon paste.

