Jan Kohlmeyer

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

A class-wide phylogenetic assessment of Dothideomycetes

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Fungal biodiversity in aquatic habitats

Fungal biodiversity in freshwater, brackish and marine habitats was estimated based on reports in the literature. The taxonomic groups treated were those with species commonly found on submerged substrates in aquatic habitats: Ascomycetes (exclusive of yeasts), Basidiomycetes, Chytridiomycetes, and the non-fungal Saprolegniales in the Class Oomycetes. Based on presence/absence data for a large number and variety of aquatic habitats, about 3,000 fungal species and 138 saprolegnialean species have been reported from aquatic habitats. The greatest number of taxa comprise the Ascomycetes, including mitosporic taxa, and Chytridiomycetes. Taxa of Basidiomycetes are, for the most part, excluded from aquatic habitats. The greatest biodiversity for all groups occurs in temperate areas, followed by Asian tropical areas. This pattern may be an artifact of the location of most of the sampling effort. The least sampled geographic areas include Africa, Australia, China, South America and boreal and tropical regions worldwide. Some species overlap occurs among terrestrial and freshwater taxa but little species overlap occurs among freshwater and marine taxa. We predict that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.

Molecular systematics of the marine Dothideomycetes

Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. Few marine species are reported from the Dothideomycetidae (e.g. Mycosphaerellaceae, Capnodiales), a group poorly studied at the molecular level. New marine lineages include the Testudinaceae and Manglicola guatemalensis in the Jahnulales. Significantly, most marine Dothideomycetes are intertidal tropical species with only a few from temperate regions on salt marsh plants (Spartina species and Juncus roemerianus), and rarely totally submerged (e.g. Halotthia posidoniae and Pontoporeia biturbinata on the seagrasses Posidonia oceanica and Cymodocea nodosum). Specific attention is given to the adaptation of the Dothideomycetes to the marine milieu, new lineages of marine fungi and their host specificity.

Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.

Detection and identification of fungi intimately associated with the brown seaweed Fucus serratus.

ABSTRACT The filamentous fungi associated with healthy and decaying Fucus serratus thalli were studied over a 1-year period using isolation methods and molecular techniques such as 28S rRNA gene PCR-denaturing gradient gel electrophoresis (DGGE) and phylogenetic and real-time PCR analyses. The predominant DGGE bands obtained from healthy algal thalli belonged to the Lindra, Lulworthia, Engyodontium, Sigmoidea/Corollospora complex, and Emericellopsis/Acremonium-like ribotypes. In the culture-based analysis the incidence of recovery was highest for Sigmoidea marina isolates. In general, the environmental sequences retrieved could be matched unambiguously to isolates recovered from the seaweed except for the Emericellopsis/Acremonium-like ribotype, which showed 99% homology with the sequences of four different isolates, including that of Acremonium fuci. To estimate the extent of colonization of A. fuci, we used a TaqMan real-time quantitative PCR assay for intron 3 of the beta-tubulin gene, the probe for which proved to be species specific even when it was used in amplifications with high background concentrations of other eukaryotic DNAs. The A. fuci sequence was detected with both healthy and decaying thalli, but the signal was stronger for the latter. Additional sequence types, representing members from the Dothideomycetes, were recovered from the decaying thallus DNA, which suggested that a change in fungal community structure had occurred. Phylogenetic analysis of these environmental sequences and the sequences of isolates and type species indicated that the environmental sequences were novel in the Dothideomycetes.

Distribution of Epichloë Typhina (Ascomycetes) and Its Parasitic Fly

Fresh and dried stromata of Epichloe typhina, the cause of choke disease of grasses, were examined for infections by a host-specific fly, Phorbia phrenione. Over 35% of 4,685 stromata from 17 count...

Lulworthiales, a new order of marine Ascomycota.

Based on molecular studies using 1031 bp of the nuclear small subunit (SSU) gene and 594 bp of the nuclear large subunit (LSU) rDNA gene and using morphological characters, the genera Lulwor- thia and Lindra are removed from Halosphaeriales and assigned to the new order Lulworthiales and new family Lulworthiaceae in the class Sordariomycetes. Eleven accepted species of Lulworthia and 6 species of Lindra are listed.

Ecological notes on fungi in Mangrove forests

Lists of all marine and terrestrial fungi described from mangrove plants are compiled and relations between these fungi and mangrove forest plants ( Avicennia, Hibiscus, Pluchea, Rhizophora ) are described. Marine ascomycetes, basidiomycetes and deuteromycetes occur on submerged parts of roots (proproots, pneumatophores), stems and branches. Six of thirty-one species appear to be host specific. Most frequent marine species are Lulworthia sp., Metasphaeria australiensis and ‘ Phoma ’ sp. The majority of the forty-four terrestrial fungi described from mangrove trees are parasites on living leaves. High contents of tannin do not protect mangrove plants from decomposition by marine fungi and wood boring animals (shipworms and isopods). Submerged bark and wood of mangroves are deteriorated by higher marine fungi. Wood destruction is of the ‘soft rot’ type. Fewer kinds of fungi occur on bark than on wood; Mycosphaerella pneumatophorae (in Avicennia ) and Keissleriella blepharospora (in Rhizophora ) are exclusively corticolous. Some fungi develop within calcareous layers of shipworm tubes in mangrove roots or branches. Rhizophora forms adventitious roots above injured and fungus-infested root tips. There is a zonation of fungi and other organisms along vertical roots, stems, or branches of mangrove trees. Submerged parts are inhabited by marine fungi, algae, balanids, worms, shipworms, and gribbles. Several species of fungi are usually found together on the submerged part of one root, but no distinct pattern of vertical distribution among the species is evident. Growth of marine and terrestrial fungi overlaps at the high tide line. Organisms above the water include ascomycetes, deuteromycetes, basidiomycetes, and lichens. Horizontal distribution of fungi in a Hawaiian mangrove swamp along a transect from salt to fresh water is described. Marine fungi are absent in the freshwater part. Thus, host specific K. blepharospora occurs only on Rhizophora plants in salt water. Dispersal and geographical distribution of mangrove fungi are discussed. Knowledge of occurrence of marine fungi in the eastern mangrove is almost absent. Some fungi, chiefly host specific ones, have a limited distribution, while omnivorous species are found in mangroves throughout the tropics and sub-tropics. Most mangrove fungi are warm water species.

Is Ascophyllum nodosum Lichenized

In a recent synopsis on Ascophyllum nodosum (L.) LE JOLIS, BAARDSETH (1970) accumulates all Information available on this common brown alga. This author rnentions briefly the presence o£ fungal hyphae that are never absent from any part o£ Ascophyllum and expresses bis uncertainty about the question if these hyphae belong t o the Asconnycete, described from Ascophyllum^ namely Mycosphaerella ascophylli COTTON (1908). The regular occurrence of an endosymbiotic fungus in all Ascophyllum plants appears to be widely unknown or unnoticed among algologists, The association is not