Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

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A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

Biology and chemistry of endophytes.

Our understanding of how saprotrophic and mycorrhizal fungi interact to re-circulate carbon and nutrients from plant litter and soil organic matter is limited by poor understanding of their spatiotemporal dynamics. In order to investigate how different functional groups of fungi contribute to carbon and nitrogen cycling at different stages of decomposition, we studied changes in fungal community composition along vertical profiles through a Pinus sylvestris forest soil. We combined molecular identification methods with 14C dating of the organic matter, analyses of carbon:nitrogen (C:N) ratios and 15N natural abundance measurements. Saprotrophic fungi were primarily confined to relatively recently (< 4 yr) shed litter components on the surface of the forest floor, where organic carbon was mineralized while nitrogen was retained. Mycorrhizal fungi dominated in the underlying, more decomposed litter and humus, where they apparently mobilized N and made it available to their host plants. Our observations show that the degrading and nutrient-mobilizing components of the fungal community are spatially separated. This has important implications for biogeochemical studies of boreal forest ecosystems.

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Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest

Biological invasions dramatically affect the distribution, abundance and reproduction of many native species. Because of these ecological effects, exotic species can also influence the evolution of natives exposed to novel interactions with invaders. Evolutionary changes in natives in response to selection from exotics are usually overlooked, yet common responses include altered anti-predator defenses, changes in the spectrum of resources and habitats used, and other adaptations that allow native populations to persist in invaded areas. Whether a native population is capable of responding evolutionarily to selection from invaders will depend on the demographic impact of the invader, the genetic architecture and genetic variability of the native population and potentially the history of previous invasions. In some cases, natives will fail to evolve or otherwise adapt, and local or global extinction will result. In other cases, adaptive change in natives may diminish impacts of invaders and potentially promote coexistence between invaders and natives. Here, we review the evidence for evolutionary responses of native species to novel community members. We also discuss how the effects of introduced species may differ from those caused by natural range expansions of native species. Notably, introduced species may come from remote biotas with no previous evolutionary history with the native community. In addition, the rate of addition of introduced species into communities is much greater than all but the most extreme cases of historical biotic exchange. Understanding the evolutionary component of exotic/native species interactions is critical to recognizing the long-term impacts of biological invasions, and to understanding the role of evolutionary processes in the assembly and dynamics of natural communities.

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Evolutionary responses of natives to introduced species: what do introductions tell us about natural communities?

For millions of years the distribution of the world's biota has been restricted by oceans and other natural barriers. During the last 100 years, human activities, especially international travel and trade, have circumvented these barriers and species are invading new continents at an increasing rate. Biological invasions of insect, plants, and fungal pest species often cause substantial disturbance to forest ecosystems and as well as severe socioeconomic impacts. The invasion process is composed of three phases: arrival, establishment, and spread. Arrival occurs when a species is initially transported to the new area (e.g. transportation to a new continent). Establishment is essentially the opposite of extinction; it is the process by which a population becomes abundant enough to prevent extinction. Spread is the process by which a species expands its range into adjoining uninfested areas. Management of pest invasions focuses on preventing arrival, establishment, or spread. We present case histories that illustrate the invasion process via details of the arrival, spread, impact, and management of selected exotic forest pests. Biological invasions are probably the most significant environmental threat to the maintenance of natural forest ecosystems in North America and elsewhere. The magnitude of this problem necessitates increased efforts to reduce the incidence and impacts of pest invasions. FOR. SCI. MONOGR. 30:1-49. ADDITIONAL

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Invasion by Exotic Forest Pests: A Threat to Forest Ecosystems

The frequency of six mechanisms of resistance to white pine blister rust is presented for 18 white pine species. The mechanisms are: prevention of needle lesions, reduced frequency of such lesions, premature shedding of infected needles, a fungicidal reaction in the short shoot, reactions that eliminate established bark infections, and the ability of a seedling to remain alive when infected. The importance of these mechanisms in selecting for resistance in the very susceptible North American white pines is discussed.

Relative blister rust resistance of white pines

Phylogenetic and genetic relationships among 10 North American Armillaria species were analysed using sequence data from ribosomal DNA (rDNA), including intergenic spacer (IGS-1), internal transcribed spacers with associated 5.8S (ITS + 5.8S), and nuclear large subunit rDNA (nLSU), and amplified fragment length polymorphism (AFLP) markers. Based on rDNA sequence data, the nLSU region is less variable among Armillaria species than the ITS + 5.8S and IGS-1 regions (nLSU < ITS + 5.8S < IGS-1). Phylogenetic analyses of the rDNA sequences suggested Armillaria mellea, A. tabescens and A. nabsnona are well separated from the remaining Armillaria species (A. ostoyae, A. gemina, A. calvescens, A. sinapina, A. gallica, NABS X and A. cepistipes). Several Armillaria species (A. calvescens, A. sinapina, A. gallica, NABS X and A. cepistipes) clustered together based on rDNA sequencing data. Based on the isolates used in this study, it appears that techniques based on IGS-1, ITS + 5.8S, and/or D-domain/3' ends of nLSU are not reliable for distinguishing A. calvescens, A. sinapina, A. gallica and A. cepistipes. However, AFLP data provided delineation among these species, and AFLP analysis supported taxonomic classification established by conventional methods (morphology and interfertility tests). Our results indicate that AFLP genetic markers offer potential for distinguishing currently recognized North American Biological Species (NABS) of Armillaria in future biological, ecological and taxonomic studies.

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Characterization of North American Armillaria species: genetic relationships determined by ribosomal DNA sequences and AFLP markers

Summary White pine blister rust disease, caused by the introduced pathogen Cronartium ribicola, has severely disrupted five-needled pine ecosystems in North America. A 100-year effort to manage this disease was predicated in part on the premise that the pathogen utilizes only species of Ribes (Grossulariaceae) as alternate hosts on this continent. The current study presents the first conclusive demonstration that some species in the family Orobanchaceae (Pedicularis racemosa and Castilleja miniata) are functioning as alternate hosts in a natural ecosystem of North America. This finding has implications for improving our understanding of epidemiology, pathogen adaptation and host‐pathogen interactions within white pine blister rust.

https://www.fs.fed.us/rm/pubs_other/rmrs_2006_mcdonald_g001.pdf

Pedicularis and Castilleja are natural hosts of Cronartium ribicola in North America: a first report

Summary The fungal community inhabiting large woody roots of healthy conifers has not been well documented. To provide more information about such communities, a survey was conducted using increment cores from the woody roots of symptomless Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa) growing in dry forests on the eastern slope of the Cascade Mountains in Washington state, USA. Fungal isolates were cultured on standard media, and then were identified using a combination of molecular and morphological methods. Fungal genera and species identified in this study will provide baseline data for future surveys of fungal endophytes. Examination of internal transcribed spacer (ITS1 and ITS2) and 5.8S rDNA sequences and morphology of cultured fungi identified 27 fungal genera. Two groups predominated: Byssochlamys nivea Westling (20.4% of isolations) and Umbelopsis species (10.4% of isolations). This is the first report of B. nivea within large woody roots of conifers. Both taxa have been previously identified as potential biological control agents. Although some trends were noted, this study found no significant evidence of host species or plant association effects on total recovery of fungal endophytes or recovery of specific fungal taxa.

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Fungal endophytes in woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa)

Whitebark pine (Pinus albicaulis) is one of many North American white pine species (Pinus subgenus Strobus) susceptible to the fungal disease white pine blister rust (Cronartium ribicola). Blister rust has caused severe mortality (often reaching nearly 100 percent) in many stands of white bark pine north of 45° latitude in western North America. The rust is slowly moving south through the range of whitebark pine and other white pine species.

https://www.fs.fed.us/rm/pubs_other/rmrs_2001_hoff_r001.pdf

Geral I. McDonald

Papers

Relative blister rust resistance of white pines

Characterization of North American Armillaria species: genetic relationships determined by ribosomal DNA sequences and AFLP markers

Pedicularis and Castilleja are natural hosts of Cronartium ribicola in North America: a first report

Fungal endophytes in woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa)

Strategies for managing whitebark pine in the presence of white pine blister rust [Chapter 17]