Basal stem rot caused by Ganoderma boninense is the single major disease to affect oil palms in South Asia and Oceania. Although first described in commercial plantations some 90 years ago it remains a major constraint to oil palm planting, with disease occurence increasing with succesive plantings. There is a considerable volume of published research into the occurence, diagnostics and control of basal stem rot but much of this has been focused on individual plantings or local environments. In this manuscript we attempt to bring together reports from across the South Asia/Oceania regions to provide a comprehensive review of the current knowledge and to identify the key issues that still need to be addressed in order to achieve a comprehensive understanding of the disease and disease processes.

This chapter deals with numerical procedures that have commonly been used in chemotaxonomic and molecular studies of filamentous fungi. In order to use a numerical algorithm to group organisms, it is necessary to first calculate a measure of resemblance between the organisms. To determine groups based on resemblance it is necessary to calculate the resemblance of each organism to each other organism. The construction of the data matrix is an important part of grouping the organisms, as this is the form in which the experimental data are analyzed. Data presented tor numerical analysis do not have to be in a binary rorm, and quantitative and qualitative values may be used directly. Probably the most commonly used resemblance coefficients are the association coefficients. There is a wide selection of distance coefficients in use with fungal taxonomic data. Many distance coefficients are based on measures of the distances between organisms in character or attribute space.

Eumycetoma is a debilitating, chronic, fungal infection that is endemic in India, Indonesia, and parts of Africa and South and Central America. It remains a neglected tropical disease in need of international recognition. Infections follow traumatic implantation of saprophytic fungi and frequently require radical surgery or amputation in the absence of appropriate treatment. Several fungal species can cause black-grain mycetomas, including Madurella spp. (Sordariales), Falciformispora spp., Trematosphaeria grisea, Biatriospora mackinnonii, Pseudochaetosphaeronema larense, and Medicopsis romeroi (all Pleosporales). We performed phylogenetic analyses based on five loci on 31 isolates from two international culture collections to establish the taxonomic affiliations of fungi that had been isolated from cases of black-grain mycetoma and historically classified as Madurella grisea Although most strains were well resolved to species level and corresponded to known agents of eumycetoma, six independent isolates, which failed to produce conidia under any conditions tested, were only distantly related to existing members of the Pleosporales Five of the six isolates shared >99% identity with each other and are described as Emarellia grisea gen. nov. and sp. nov; the sixth isolate represents a sister species in this novel genus and is described as Emarellia paragrisea. Several E. grisea isolates were present in both United Kingdom and French culture collections and had been isolated independently over 6 decades from cases of imported eumycetoma. Four of the six isolates involved patients that had originated on the Indian subcontinent. All isolates were all susceptible in vitro to the azole antifungals, but had elevated MICs with caspofungin.

Variation of 45 Gibberella xylarioides cultures isolated from coffee trees in Africa was assessed by sequencing the partial translation elongation factor gene, by A + T rich DNA restriction fragment length polymorphism (RFLP) analysis and by inter-simple sequence repeat polymerase chain fingerprinting. Results were analysed in relation to host plant species and mating compatibilities to determined biological species (BS). Additionally, five “historical” strains isolated prior to the 1990s, and considered to belong to G. xylarioides , were obtained from internationally-recognised culture collections and a further 10 strains of various Gibberella / Fusarium spp., isolated from Coffea spp., were included to provide contextual comparisons. Ribosomal intergenic spacer (IGS) sequencing was undertaken for representatives of the suggested BS. Results confirmed all strains as G. xylarioides and that strains of sterile group 4 (SG4) may represent one or more additional “cryptic” species. ISSR fingerprints showed a single host correlated difference, suggesting stable clonal spread and this was supported by consistent A + T rich DNA band patterns for all strains. In contrast the IGS sequences identified potential phylogenetic events correlated to BS.

The causal organism responsible for severe outbreaks of orchid anthracnose in India, which affectes leaves, petioles and blooms, is not clearly established. Ten Colletotrichum isolates recovered from different orchid species in the Sikkim state were characterized based on morphological and a multilocus molecular phylogenetic analysis of the rDNA-ITS region (ITS), partial actin (ACT) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) sequences. Phylogeny inferred from combined datasets of ACT, ITS and GAPDH revealed two groups, representing Colletotrichum cymbidiicola and C. cliviae. Cultural and morphological characters are presented for these two species. Pathogenicity assays confirmed that both species isolated from orchids are the causal agents of anthracnose. The occurrence of C. cymbidiicola and C. cliviae is reported for the first time on orchids in India.

To date over 1 000 non-lichenized fungal species have been recorded by collection or isolation from Antarctica, and additional taxa are now being identified by molecular studies. The number and variety of species recorded so far suggest that the fungi may be the most diverse biota in the Antarctic, and the additional taxa identified by molecular surveys suggest that the true diversity may be far greater than is currently estimated. Fungi occupy many different ecological niches in the Antarctic, and their significance in these niches is only poorly understood. The majority of species described from the region have been identified as members of broadly cosmopolitan groups, but there is some evidence for both endemic strains and populations. This review brings together the current broad systematic and ecological findings for the non-lichenized Antarctic fungi. (C) 2012 Elsevier Ltd and The British Mycological Society.

Volutella colletotrichoides is shown to belong to the Plectosphaerellaceae rather than the Hypocreales where other species of that genus reside. The new genus Lectera is described for V. colletotrichoides, and for a further, previously undescribed species with slightly longer conidia and differences in rDNA ITS and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) sequences. Lectera species are found to be soil-dwelling organisms associated particularly with species of Fabaceae, and L. colletotrichoides is demonstrated to be a pathogen of Cicer arietinum and other grain legumes.

Changes in mouth pressure during flow interruption (Pmo transients) can be used to assess airway resistance (Rint). Initial pressure oscillations can cause difficulties in estimating Rint but are themselves a marker of airway status as their amplitude increases [1] with bronchodilator (BD) and decreases with methacholine [2]. To investigate this measurement, we analysed Pmo transients pre- and post- bronchodilator in 13 preschool children with recurrent wheeze on 2 separate visits 4 weeks apart. The median (range) age of the children at the first visit was 52 months (38 to 64 months). The amplitude of the first upward oscillation as a proportion of end-interruption pressure was calculated and compared with Rint calculated by linear back extrapolation. The median value of at least 5 acceptable transients was assessed for amplitude (Posc) and Rint by linear back extrapolation (LBE30/70). Posc increased significantly (paired t-test) with BD both at visit 1, with mean (SD) pre 1.38 (0.25), post 1.63 (0.32) and visit 2, with pre 1.39 (0.29), post 1.61 (0.37). LBE30/70 decreased significantly with BD both at visit 1, mean (SD) pre 1.08 (0.27), post 0.88 (0.21) and at visit 2, pre 1.08 (0.26), post 0.92 (0.22). However there was no significant relation between Posc change and LBE30/70 change in response to BD (Pearson9s correlation coefficient). These results suggest that Pmo oscillation amplitude after flow interruption may provide an alternative measure of airway mechanics which merits further study. References: 1Bridge PD et al. Pediatr Pulmonol 2005; 40:420–425. 2Kivastik J et al. Clin Physiol Funct Imaging 200; 29:45-52.

To understand fully the risk of biological invasions, it is necessary to quantify propagule pressure along all introduction pathways. In the Antarctic region, importation of fresh produce is a potentially high risk, but as yet unquantified pathway. To address this knowledge gap, >11,250 fruit and vegetables sent to nine research stations in Antarctica and the sub-Antarctic islands, were examined for associated soil, invertebrates and microbial decomposition. Fifty-one food types were sourced from c. 130 locations dispersed across all six of the Earth’s inhabited continents. On average, 12% of food items had soil on their surface, 28% showed microbial infection resulting in rot and more than 56 invertebrates were recorded, mainly from leafy produce. Approximately 30% of identified fungi sampled from infected foods were not recorded previously from within the Antarctic region, although this may reflect limited knowledge of Antarctic fungal diversity. The number of non-native flying invertebrates caught within the Rothera Research Station food storage area was linked closely with the level of fresh food resupply by ship and aircraft. We conclude by presenting practical biosecurity measures to reduce the risk of non-native species introductions to Antarctica associated with fresh foods.

Aims:To characterize and identify a novel contaminant of aviation fuel.Methods and Results:Micro-organisms (yeasts and bacteria) were isolated from samples of aviation fuel. A yeast that proved to have been unrecorded previously was isolated from more than one fuel sample. This novel yeast proved to be a new species of Candida and is described here. Ribosomal RNA gene sequence analyses of internal transcribed spacer (ITS) regions (including 5 center dot 8S subunit) plus the 26S D1/D2 domains showed the strains to cluster within the Candida membranifaciens clade nearest to, but distinct from, Candida tumulicola. Phenotypic tests were identical for both isolates. Physiological and biochemical tests supported their position as a separate taxon. The yeast was assessed for its effect on the main constituent hydrocarbons of aviation fuel.Conclusions:Two strains (IMI 395605T and IMI 395606) belonging to the novel yeast species, Candida keroseneae, were isolated from samples of aircraft fuel (kerosene), characterized and described herein with reference to their potential as contaminants of aviation fuel.Significance and Impact of the Study:As a result of isolating a novel yeast from aviation fuel, the implications for microbial contamination of such fuel should be considered more widely than previously thought.

The leafy liverwort Lophozia excisa , which is colonised by basidiomycete fungi in other biomes and which evidence suggests may be colonised by mycorrhizal fungi in Antarctica, was sampled from Léonie Island in the southern maritime Antarctic (67°36′ S, 68°21′ W). Microscopic examination of plants indicated that fungal hyphae colonised 78% of the rhizoids of the liverwort, apparently by entering the tips of rhizoids prior to growing into their bases, where they formed hyphal coils. Extensive colonisation of stem medullary cells by hyphae was also observed. DNA was extracted from surface-sterilised liverwort tissues and sequenced following nested PCR, using the primer set ITS1F/TW14, followed by a second round of amplification using the ITSSeb3/TW13 primer set. Neighbour-joining analyses showed that the sequences obtained nested in Sebacinales clade B as a 100% supported sister group to Sebacinales sequences from the leafy liverworts Lophozia sudetica , L. incisa and Calypogeia muelleriana sampled from Europe. Direct PCR using the fungal specific primer set ITS1F/ITS4 similarly identified fungi belonging to Sebacinales clade B as the principal colonists of L. excisa tissues. These observations indicate the presence of a second mycothallus in Antarctica and support the previous suggestion that the Sebacinales has a wide geographical distribution.

Interrupter resistance (R(int)) is a useful measure of airway caliber in young children, but has not been well characterized in infants-in whom there are concerns about the accurate measurement of driving pressure. This study aimed to assess the feasibility and repeatability of measuring R(int) in unsedated newborn infants, and to explore alternative algorithms for calculating driving pressure. R(int) measurement was attempted in 28 healthy term newborn infants during natural sleep using the MicroRint device. Paired R(int) measurements were achieved in 24 infants, but after screening of waveforms only 15 infants had at least 5 technically acceptable waveforms on both measurements. R(int) values obtained were comparable with reported values for airflow resistance in newborns using other methods. However, the repeatability coefficient (CR) was much higher than reported values in preschool children using standard back-extrapolation algorithms, with CR 2.47 KPa L(-1) sec (unscreened) and 2.93 KPa L(-1) sec (screened). Other algorithms gave only marginally better repeatability, with all CR values over 50% of the mean R(int) value. Using current commercially available equipment, R(int) is too poorly repeatable to be a reliable measurement of airflow resistance in newborn infants. Lower deadspace equipment is needed, but anatomical and physiological factors in the infant are also important.

Bacterial community composition was determined by culture-independent PCR-based methods in two soils differing markedly in their water, C, N and P contents sampled from Mars Oasis on Alexander Island, western Antarctic Peninsula. 16S rRNA sequences of the phyla Actinobacteria, Cyanobacteria, α-Proteobacteria and Acidobacteria were commonly (>8% frequency) obtained from soil. Those of β-, γ- and δ-Proteobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, Planctomycetes, Gemmatimonadetes and Firmicutes were less frequent. Comparisons of slopes of collector's curves and the Shannon–Weiner diversity index indicated no difference in overall bacterial diversity between the two soils, although sequences of δ-Proteobacteria and the cyanobacterial genus Leptolyngbya were more commonly derived from the soil with the higher water and nutrient content. The data suggest that different levels of soil water, C, N and P have only a minor effect on the bacterial community composition of maritime Antarctic soils.