Rajesh Jeewon

A Phylogenetic Evaluation of Whether Endophytes Become Saprotrophs at Host Senescence

Fungal endophytes and saprotrophs generally play an important ecological role within plant tissues and dead plant material. Several reports based solely on morphological observations have postulated that there is an intimate link between endophytes and saprotrophs. This study aims to provide valuable insight as to whether some endophytic fungi manifest themselves as saprotrophs upon host decay. Ribosomal DNA-based sequence comparison and phylogenetic relationships from 99 fungal isolates (endophytes, mycelia sterilia, and saprotrophs) recovered from leaves and twigs of Magnolia liliifera were investigated in this study. Molecular data suggest there are fungal taxa that possibly exist as endophytes and saprotrophs. Isolates of Colletotrichum, Fusarium, Guignardia, and Phomopsis, which are common plant endophytes, have high sequence similarity and are phylogenetically related to their saprotrophic counterparts. This provides evidence to suggest that some endophytic species change their ecological strategies and adopt a saprotrophic lifestyle. The implication of these findings on fungal biodiversity and host specificity is also discussed.

The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts

Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.

Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters.

The taxonomy of the coelomycetous fungus Pestalotiopsis and other closely related genera based on morphological characters has been equivocal. To gain insight in the phylogenetic relationships of Pestalotiopsis and its allies, part of the large subunit (28S) ribosomal DNA region was examined and compared with existing morphological information. Phylogenetic analyses were conducted using parsimony, distance, and likelihood criteria. Results of the analyses showed that Bartalinia, Pestalotiopsis, Seimatosporium, and Seiridium represent distinct monophyletic groups with high bootstrap support. However, Truncatella species are paraphyletic with Bartalinia, sharing a common ancestor. Pestalotia species sequenced clustered together with Pestalotiopsis. These genera should be recognized as distinct natural groups except for Monochaetia and Discosia, which need to be further resolved. Tree topologies are generally in concordance with previous morphological hypotheses, most notably the placement of all Pestalotia species, except the type P. pezizoides, in Pestalotiopsis. Well-supported clades corresponding to groupings based on conidial morphology were resolved and the relative importance of morphological characters for generic delimitation is discussed. Molecular data also provide further evidence to support the association of these coelomycetes with the Amphisphaeriaceae.

Overweight and Obesity Epidemic in Developing Countries: A Problem with Diet, Physical Activity, or Socioeconomic Status?

Obesity is a significant public health concern affecting more than half a billion people worldwide. Obesity rise is not only limited to developed countries, but to developing nations as well. This paper aims to compare the mean body mass index trends in the World Health Organisation- (WHO-) categorised regions since 1980 to 2008 and secondly to appraise how socioeconomic disparities can lead to differences in obesity and physical activity level across developing nations. Taking into account past and current BMI trends, it is anticipated that obesity will continue to take a significant ascent, as observed by the sharp increase from 1999 to 2008. Gender differences in BMI will continue to be as apparent, that is, women showing a higher BMI trend than men. In the coming years, the maximum mean BMI in more developed countries might be exceeded by those in less developed ones. Rather than focusing on obesity at the individual level, the immediate environment of the obese individual to broader socioeconomic contexts should be targeted. Most importantly, incentives at several organisational levels, the media, and educational institutions along with changes in food policies will need to be provided to low-income populations.

Families of Sordariomycetes

Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi characterized mainly by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, coprophilous and fungicolous, lichenized or lichenicolous taxa. They occur in terrestrial, freshwater and marine habitats worldwide. This paper reviews the 107 families of the class Sordariomycetes and provides a modified backbone tree based on phylogenetic analysis of four combined loci, with a maximum five representative taxa from each family, where available. This paper brings together for the first time, since Barrs’ 1990 Prodromus, descriptions, notes on the history, and plates or illustrations of type or representative taxa of each family, a list of accepted genera, including asexual genera and a key to these taxa of Sordariomycetes. Delineation of taxa is supported where possible by molecular data. The outline is based on literature to the end of 2015 and the Sordariomycetes now comprises six subclasses, 32 orders, 105 families and 1331 genera. The family Obryzaceae and Pleurotremataceae are excluded from the class.

Sequence data reveals phylogenetic affinities of fungal anamorphs Bahusutrabeeja, Diplococcium, Natarajania, Paliphora, Polyschema, Rattania and Spadicoides

Partial 28S rRNA gene sequence-data of the strains of the anamorphic genera Bahusutrabeeja, Diplococcium, Natarajania, Paliphora, Polyschema, Rattania and Spadicoides were analysed to predict their phylogenetic relationships and taxonomic placement within the Ascomycota. Results indicate that Diplococcium and morphologically similar genera, i.e. Spadicoides, Paliphora and Polyschema do not share a recent common ancestor. The type species of Diplococcium, D. spicatum is referred to Helotiales (Leotiomycetes). The placement of Spadicoides bina, the type of the genus, is unresolved but it is shown to be closely associated with Porosphaerella species, which are sister taxa to Coniochaetales (Sordariomycetes). Three Polyschema species analysed in this study represent a monophyletic lineage and are related to Lentithecium fluviatile and Leptosphaeria calvescens in Pleosporales (Dothideomycetes). DNA sequence analysis also suggests that Paliphora intermedia is a member of Chaetosphaeriaceae (Sordariomycetes). The type species of Bahusutrabeeja, B. dwaya, is phylogenetically related to Neodeightonia (=Botryosphaeria) subglobosa in Botryosphaeriales (Dothideomycetes). Monotypic genera Natarajania and Rattania are phylogenetically related to members of Diaporthales and Chaetosphaeriales, respectively. Future studies with extended gene datasets and type strains are required to resolve many novel but morphologically unexplainable phylogenetic scenarios revealed from this study. It is increasingly becoming evident that a fungal lineage may include a mosaic of anamorphs, teleomorphs and pleomorphs whose morphologies may not always be correlated. It is therefore suggested that where possible all new species descriptions, whether teleomorphic, anamorphic or pleomorphic, should include DNA sequence-data to facilitate amalgamation of anamorphic and pleomorphic genera in a single phylogenetic classification system.

Molecular systematics of the Amphisphaeriaceae based on cladistic analyses of partial LSU rDNA gene sequences.

The Amphisphaeriaceae is an important family of ascomycetes within the Xylariales. There has been, however, disagreement regarding the taxonomic placement of many genera within this family and whether it should be confined to ascomycetes producing Pestalotiopsis-like anamorphs. In this study, phylogenetic relationships among members of the Amphisphaeriaceae are investigated using partial sequences of the 28S rDNA. Molecular data provided further evidence to support the association of several coelomycetous genera with the ascomycetous Amphisphaeriaceae. Phylogenetic analyses also show that all ascomycetous genera possessing Pestalotiopsis-like anamorphs are monophyletic and confirm the anamorphic-teleomorphic connections of some. There is, however, insufficient evidence to support the restriction of Amphisphaeriaceae to genera, which produce Pestalotiopsis-like anamorphs, because the phylogenetic placement of Amphisphaeria umbrina is not fully resolved and its affinities with other members received low bootstrap support. The results also indicate that Iodosphaeria and Arecophila should be excluded from the Amphisphaeriaceae. The placement of Lanceispora in the Amphisphaeriaceae is doubtful. A broad concept of the family Amphisphaeriaceae is advocated until further data are available.

An Assessment of the Breastfeeding Practices and Infant Feeding Pattern among Mothers in Mauritius

Proper breastfeeding practices are effective ways for reducing childhood morbidity and mortality. While many mothers understand the importance of breastfeeding, others are less knowledgeable on the benefits of breastfeeding and weaning. The aim in here is to assess breastfeeding pattern, infant formula feeding pattern, and weaning introduction in Mauritius and to investigate the factors that influence infant nutrition. 500 mothers were interviewed using a questionnaire which was designed to elicit information on infant feeding practices. Statistical analyses were done using SPSS (version 13.0), whereby chi-square tests were used to evaluate relationships between different selected variables. The prevalence of breastfeeding practice in Mauritius has risen from 72% in 1991 to 93.4% as found in this study, while only 17.9% breastfed their children exclusively for the first 6 months, and the mean duration of EBF (exclusive breastfeeding) is 2.10 months. Complementary feeding was more commonly initiated around 4–6 months (75.2%). Despite the fact that 60.6% of mothers initiate breastfeeding and 26.1% of mothers are found to breastfeed up to 2 years, the practice of EBF for the first 6 months is low (17.9%). Factors found to influence infant feeding practices are type of delivery, parity, alcohol consumption, occupation, education, and breast problems.

Multi-gene phylogeny and morphotaxonomy of Amniculicola lignicola: a novel freshwater fungus from France and its relationships to the Pleosporales.

A collection of submerged wood samples in the Pyrénées, France, led to the discovery of a new freshwater Dothideomycetes genus. Amniculicola lignicola gen sp. nov, is described and illustrated. In addition, rDNA and RPB2 gene sequences are analysed phylogenetically to investigate its ordinal and familial placement. Morphologically, Amniculicola resembles species of Ostropella and Xenolophium in having subglobose ascomata with prominent lips surrounding a slit-like ostiole. However, it is readily distinguished from Ostropella and Xenolophium by ascus shape and in having a short pedicle and thin peridium. Phylogenetic analyses based on 28S rDNA sequences also indicated that A. lignicola and O. albocincta (type species of Ostropella) are phylogenetically distinct. Morphological characters indicate that Amniculicola belongs in the Pleosporales and this is supported by molecular data. Sequences analyses from three loci suggest that it is closely related to anamorphic fungi, such as Anguillospora longissima, Spirosphaera cupreorufescens, and Repetophragma ontariense; however, its affinities with known Dothideomycetes and its familial placement are still unresolved.

An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence

The previous phylogenies of Sordariomycetes by M.E. Barr, O.E. Eriksson and D.L. Hawksworth, and T. Lumbsch and S. Huhndorf, were mainly based on morphology and thus were somewhat subjective. Later outlines by T. Lumbsch and S. Huhndorf, and Maharachchikumbura and co-authors, took into account phylogenetic evidence. However, even these phylogenetic driven arrangements for Sordariomycetes, were somewhat subjective, as the arrangements in trees depended on many variables, such as number of taxa, different gene regions and methods used in the analyses. What is needed is extra evidence to help standardize ranking in the fungi. Estimation of divergence times using molecular clock methods has been proposed for providing additional rational for higher ranking of taxa. Thus, in Sordariomycetes, a divergence period (i.e. 200–300 MYA) can be used as criteria to judge when a group of related taxa evolved and what rank they should be given. In this paper, we provide an updated classification of accepted subclasses, orders of Sordariomycetes and use divergence times to provide additional evidence to stabilize ranking of taxa in the class. We point out and discuss discrepancies where the phylogenetic tree conflicts with the molecular clock.