A new approximate matrix factorization for implicit time integration in air pollution modeling

Implicit time stepping typically requires solution of one or several linear systems with a matrix I−τJ per time step where J is the Jacobian matrix. If solution of these systems is expensive, replacing I−τJ with its approximate matrix factorization (AMF) (I−τR)(I−τV), R+V=J, often leads to a good compromise between stability and accuracy of the time integration on the one hand and its efficiency on the other hand. For example, in air pollution modeling, AMF has been successfully used in the framework of Rosenbrock schemes. The standard AMF gives an approximation to I−τJ with the error τ2RV, which can be significant in norm. In this paper we propose a new AMF. In assumption that −V is an M-matrix, the error of the new AMF can be shown to have an upper bound τ||R||, while still being asymptotically $O(\tau^2)$. This new AMF, called AMF+, is equal in costs to standard AMF and, as both analysis and numerical experiments reveal, provides a better accuracy. We also report on our experience with another, cheaper AMF and with AMF-preconditioned GMRES

Arbuscular mycorrhizal fungi in organic systems

Arbuscular mycorrhizal fungi (AMF) are potential contributors to plant nutrition and pathogen suppression in low input agricultural systems, although individual species of AMF vary widely in their functional attributes. Recent studies at HRI and elsewhere have suggested that in some agricultural systems inoculum of AMF is substantially lower under conventional management relative to that under organic management. Further studies have suggested that conventional management selects AMF communities with limited benefits to their plant hosts relative to those in organic systems. There is a need to investigate the generality of these findings, and their implications for the productivity of organic systems, particularly during the period following conversion to organic management. The current project was designed to pull together existing understanding of the role, and potential role, of AMF in organic systems, and to identify sites and develop methods for use in a subsequent research programme. The project had three objectives: 01 To deliver a literature review covering current knowledge of the role of AMF in conventional and organic agricultural systems. The review considered the ways in which management influences the structure and functioning of AMF communities, including their contributions under conventional and organic management, and recommendations for future research needs. 02 To establish the extent of differences in AMF inoculum between organic and conventional systems, covering a range of management practices. Paired organic and conventional fields at 12 sites from across England were selected to investigate the relationships between management, AMF communities and soil chemistry. Organic and conventionally managed soils showed no significant difference in soil chemical properties (Organic C, total N, total P, extractable P, K, Mg). However, organically managed soils had greater AMF spore numbers and root colonisation potential, and therefore higher AMF inoculum potential, than conventionally managed soil. The relative difference in AMF spore numbers between organic and conventionally managed fields increased with time since conversion. Differences in AMF inoculum potential between organic and conventionally managed fields, and between farm sites, could not be related to differences in soil chemistry. 03 To develop a method suitable for characterising AM fungus communities in soil libraries, based on 18S rRNA terminal restriction fragment length polymorphism (T-RFLP) T-RFLP was shown to provide a rapid semi-quantitative method for analysis of AMF community diversity. However it was clear that primers currently used to amplify AMF are selective and do not allow diversity of the whole AMF community to be determined. Additionally these primers amplify contaminant fungi which need to be removed from the T-RFLP profile prior to analysis. However, contaminant diversity was shown to be low. The project has identified sites and techniques which could be valuable in future research to study the role of AMF under organic management. The study has also highlighted a number of key areas in which further research is needed in order to harness AMF to improve sustainability and productivity of organic and other agricultural systems. In particular, there is a need to determine the extent to which AMF diversity varies between organic and conventional management, the rate and mechanisms by which AMF diversity increases following conversion to organic production, the relationships between AMF diversity and crop nutrition/ pathogen control, and the soil factors controlling the effectiveness of AMF inoculum

Improving approximate matrix factorizations for implicit time integration in air pollution modelling

For a long time operator splitting was the only computationally feasible way of implicit time integration in large scale Air Pollution Models. A recently proposed attractive alternative is Rosenbrock schemes combined with Approximate Matrix Factorization (AMF). With AMF, linear systems arising in implicit time stepping are solved approximately in such a way that the overall computational costs per time step are not higher than those of splitting methods. We propose and discuss two new variants of AMF. The first one is aimed at yet a further reduction of costs as compared with conventional AMF. The second variant of AMF provides in certain circumstances a better approximation to the inverse of the linear system matrix than standard AMF and requires the same computational work

The effects of arbuscular mycorrhizal fungi (AMF) and Rhizophagus irregularis on soil microorganisms assessed by metatranscriptomics and metaproteomics

Arbuscular mycorrhizal fungi (AMF) form symbioses with approximately 80% of plant species and potentially benefit their hosts (e.g. nutrient acquisition) and the soil environment (e.g. soil aggregation). AMF also affect soil microbiota and soil multifunctionality. We manipulated AMF presence (via inoculation of non-sterile soil with Rhizophagus irregularis and using a hyphal compartment design) and used RNA-seq and metaproteomics to assess AMF roles in soil. The results indicated that AMF drove an active soil microbial community expressing transcripts and proteins related to nine metabolic functions, including the metabolism of C and N. We suggest two possible mechanisms: 1) the AMF hyphae produce exudates that select a beneficial community, or, 2) the hyphae compete with other soil microbes for available nutrients and consequently induce the community to mineralize nutrients from soil organic matter. We also identified candidate proteins that are potentially related to soil aggregation, such as Lpt and HSP60. Our results bridge microbial ecology and ecosystem functioning. We show that the AMF hyphosphere contains an active community related to soil respiration and nutrient cycling, thus potentially improving nutrient mineralization from soil organic matter and nutrient supply to the plants

Effect of tillage and crop on arbuscular mycorrhiza

Large-scale inoculation with arbuscular mycorrhizal fungi (AMF) is generally impractical in most regions and we have little understanding of the factors that determine inoculation success. Nevertheless, the ability to take full advantage of indigenous AMF for sustainable production needs to be developed within cropping systems. We used part of a long-term field experiment to understand the influence of tillage and the preceding crop on AMF colonization over the growing season. Arbuscular mycorrhiza colonization rate was more affected by treatment (tillage or the combination of crop and preceding crop) than by the total number of AMF spores in the soil. Conventional tillage (CT) had a statistically significant negative effect (P £ 0.05) on spore numbers isolated from the soil, but only in the first year of study. However, the AMF colonization rate was significantly reduced by CT, and the roots of wheat, Triticum aestivum, L, cv. Coa after sunflower, Helianthus annuus L., were less well colonized than were those of triticale, X Triticosecale Wittmack, cv. Alter after wheat, but the affect of tillage was more pronounced than was the effect of crop combination. Under no-till there was a significant increase in AMF colonization rate throughout the sampling period in both wheat and triticale,indicating that the extraradical mycelium previously produced acted as a source of inoculum. In general, triticale showed greater AMF colonization than wheat, despite the preceding crop being less mycotrophic. Under these experimental conditions, typical of Mediterranean agricultural systems, AMF colonization responded more strongly to tillage practices than to the combination of crop and preceding crop

Adsorption of aminefluorides on human enamel

Changes in surface characteristics of ground and polished human enamel after adsorption of two types of aminefluorides (AmF 297 and AmF 335) have been studied. After adsorption of aminefluorides from solutions with concentrations up to 10 mM for 2 min followed by rinsing of the surface with distilled water, contact angle measurements were carried out to yield surface free energies and ellipsometry was performed to yield the adsorbed layer thickness. In a separate experiment on powdered enamel, set up in an analogous way, zeta potential changes after adsorption of aminefluorides were determined in a 10 mM potassium phosphate buffer at pH 7·0. Surface free energies decreased from 88 erg·cm−2 to 52 erg·cm−2 and 35 erg·cm−1 after adsorption of AmF 297 and AmF 335 respectively at c = 1 mM. Increasing the aminefluoride concentration in solution did not affect the values obtained. Zeta potentials, originally −36 mV, became positive after adsorption, while ellipsometry indicated the buildup of adsorbed layers with a thickness between 3 run and 12 nm. All three types of experiments indicated that both AmF 297 and AmF 335 form an adsorbed monolayer on ground and polished enamel at a concentration of 1 mM. Negligible additional adsorption takes place at higher concentrations under the present experimental circumstances. In vivo, adsorbed aminefluoride layers will be rapidly covered by adsorbed protein layers, shielding both the adsorbed aminefluoride layer as well as its physicochemical characteristics. This effect has been studied in vivo by measuring surface free energy changes of ground and polished enamel, with AmF 297 and AmF 335 adsorbed at c = 2·5 mM as a function of the time, these samples were carried by test persons in partial dentures. On both types of AmF-coated enamel the surface free energies increased within 30 min to values approaching the one obtained previously for pellicle-coated ground and polished enamel (110 ± 9 erg·cm−2)

Revealing natural relationships among arbuscular mycorrhizal fungi: culture line BEG47 represents Diversispora epigaea, not Glomus versiforme

Background: Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified. Methodology/Principal Findings: Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as ‘G. versiforme BEG47’. We show by morphological comparisons, based on type material, collected 1860–61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora. Conclusions: This study highlights that experimental works published during the last >25 years on an AMF named ‘G. versiforme’ or ‘BEG47’ refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF ‘laboratory strains’. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description

The contradictions of the Asian Monetary Fund

Focuses on the issue of an Asian Monetary Fund (AMF). At the time of its launch in March 2010, the Chiang Mai Initiative Multilateralisation (CMIM) was widely reported, particularly in Asia, as heralding the establishment of an AMF that would provide both an independent alternative to the IMF and distance from the influence of the USA. However, while the CMIM may well be a major step towards the establishment of such an AMF, as presently constituted it is neither separate from the IMF nor fully functional

Epiparasitic plants specialized on arbuscular mycorrhizal fungi

Over 400 non-photosynthetic species from 10 families of vascular plants obtain their carbon from fungi and are thus defined as myco-heterotrophs. Many of these plants are epiparasitic on green plants from which they obtain carbon by 'cheating' shared mycorrhizal fungi. Epiparasitic plants examined to date depend on ectomycorrhizal fungi for carbon transfer and exhibit exceptional specificity for these fungi, but for most myco-heterotrophs neither the identity of the fungi nor the sources of their carbon are known. Because many myco-heterotrophs grow in forests dominated by plants associated with arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), we proposed that epiparasitism would occur also between plants linked by AMF. On a global scale AMF form the most widespread mycorrhizae, thus the ability of plants to cheat this symbiosis would be highly significant. We analysed mycorrhizae from three populations of Arachnitis uniflora (Corsiaceae, Monocotyledonae), five Voyria species and one Voyriella species (Gentianaceae, Dicotyledonae), and neighbouring green plants. Here we show that non-photosynthetic plants associate with AMF and can display the characteristic specificity of epiparasites. This suggests that AMF mediate significant inter-plant carbon transfer in nature

A review of the influence of root-associating fungi and root exudates on the success of invasive plants

Plant-fungal interactions are essential for understanding the distribution and abundance of plants species. Recently, arbuscular mycorrhizal fungal (AMF) partners of non-indigenous invasive plants have been hypothesized to be a critical factor influencing the invasion processes. AMF are known to improve nutrient and moisture uptake, as well as disrupt parasitic and pathogenic microbes in the host plant. Such benefits may enable invaders to establish significant and persistent populations in environments previously dominated by natives. Coupling these findings with studies on invader pathogen-disrupting root exudates is not well documented in the literature describing plant invasion strategies. The interaction effects of altered AMF associations and the impact of invader root exudates would be more relevant than understanding the AMF dynamics or the phytochemistry of successful invaders in isolation, particularly given that AMF and root exudates can have a similar role in pathogen control but function quite differently. One means to achieve this goal is to assess these strategies concurrently by characterizing both the general (mostly pathogens or commensals) and AM-specific fungal colonization patterns found in field collected root samples of successful invaders, native plants growing within dense patches of invaders, and native plants growing separately from invaders. In this review I examine the emerging evidence of the ways in which AMF-plant interactions and the production of defensive root exudates provide pathways to invasive plant establishment and expansion, and conclude that interaction studies must be pursued to achieve a more comprehensive understanding of successful plant invasion