D. Lee Taylor

Towards a unified paradigm for sequence‐based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.

Host Specificity in Ectomycorrhizal Communities: What Do the Exceptions Tell Us?

Abstract Classic ectomycorrhizal symbioses are mutualisms that involve the exchange of fixed carbon for mineral nutrients between plant roots and fungi. They are unique in the way they contain features of both intimate and diffuse symbioses. The degree of host specificity varies, particularly among the fungi. Here we examine two exceptional cases of specificity to see what they tell us about the advantages of specificity, how it is initiated, and the potential role that it plays in complex ecosystems. The first case involves non-photosynthetic epiparasitic plants, which contrary to virtually all other plants, exhibit high levels of specificity toward their fungal hosts. The second case involves suilloid fungi; this is the largest monophyletic group of ectomycorrhizal fungi that is essentially restricted to associations with a single plant family. In both cases, new symbioses are initiated by dormant propagules that are stimulated to germinate by chemical cues from the host. This reduces the cost of wasting propagules on non-hosts. The advantages of specificity remain unclear in both cases, but we argue that increased benefit to the specialist may result from specialized physiological adaptations. We reexamine the idea that specialist fungi may help their hosts compete in complex ecosystems by reducing facultative epiparasitism by other plants, and suggest an alternative hypothesis for the observed pattern.

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied various measures of spatial pattern to characterize distributions at EMF community and species levels: Mantel tests, Mantel correlograms, variance/mean and standardized variograms. Mantel tests indicated that in four of eight sites community similarity decreased with distance, whereas Mantel correlograms also found spatial autocorrelation in those four plus two additional sites. In all but one of these sites elevated similarity was evident only at relatively small spatial scales (< 2.6 m), whereas one exhibited a larger scale pattern ( approximately 25 m). Evenness of biomass distribution among cores varied widely among taxa. Standardized variograms indicated that most of the dominant taxa showed patchiness at a scale of less than 3 m, with a range from 0 to < or =17 m. These results have implications for both sampling scale and intensity to achieve maximum efficiency of community sampling. In the systems we examined, cores should be at least 3 m apart to achieve the greatest sampling efficiency for stand-level community analysis. In some cases even this spacing may result in reduced sampling efficiency arising from patterns of spatial autocorrelation. Interpretation of the causes and significance of these patterns requires information on the genetic identity of individuals in the communities.

An empirical test of partner choice mechanisms in a wild legume–rhizobium interaction

Mutualisms can be viewed as biological markets in which partners of different species exchange goods and services to their mutual benefit. Trade between partners with conflicting interests requires mechanisms to prevent exploitation. Partner choice theory proposes that individuals might foil exploiters by preferentially directing benefits to cooperative partners. Here, we test this theory in a wild legume–rhizobium symbiosis. Rhizobial bacteria inhabit legume root nodules and convert atmospheric dinitrogen (N2) to a plant available form in exchange for photosynthates. Biological market theory suits this interaction because individual plants exchange resources with multiple rhizobia. Several authors have argued that microbial cooperation could be maintained if plants preferentially allocated resources to nodules harbouring cooperative rhizobial strains. It is well known that crop legumes nodulate non-fixing rhizobia, but allocate few resources to those nodules. However, this hypothesis has not been tested in wild legumes which encounter partners exhibiting natural, continuous variation in symbiotic benefit. Our greenhouse experiment with a wild legume, Lupinus arboreus, showed that although plants frequently hosted less cooperative strains, the nodules occupied by these strains were smaller. Our survey of wild-grown plants showed that larger nodules house more Bradyrhizobia, indicating that plants may prevent the spread of exploitation by favouring better cooperators.

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine‐scale niche partitioning

Fungi play key roles in ecosystems as mutualists, pathogens, and decomposers. Current estimates of global species richness are highly uncertain, and the importance of stochastic vs. deterministic forces in the assembly of fungal communities is unknown. Molecular studies have so far failed to reach saturated, comprehensive estimates of fungal diversity. To obtain a more accurate estimate of global fungal diversity, we used a direct molecular approach to census diversity in a boreal ecosystem with precisely known plant diversity, and we carefully evaluated adequacy of sampling and accuracy of species delineation. We achieved the first exhaustive enumeration of fungi in soil, recording 1002 taxa in this system. We show that the fungus : plant ratio in Picea mariana forest soils from interior Alaska is at least 17:1 and is regionally stable. A global extrapolation of this ratio would suggest 6 million species of fungi, as opposed to leading estimates ranging from 616 000 to 1.5 million. We also find that clos...

Population, habitat and genetic correlates of mycorrhizal specialization in the ‘cheating’ orchids Corallorhiza maculata and C. mertensiana

Unlike photosynthetic plants, several distantly related nonphotosynthetic plants are highly specialized toward their mycorrhizal fungi. It is unknown whether this specialization varies geographically or is influenced by the environment. We have investigated these questions in the nonphotosynthetic orchids Corallorhiza maculata and C. mertensiana by amplifying fungal internal transcribed spacer (ITS) fragments from widespread mycorrhiza samples and then discriminating putative fungal species using ITS restriction fragment length polymorphisms (RFLPs). Three fungal species were found across 27 plants representing seven populations of C. mertensiana; 20 species were found across 104 plants and 21 populations of C. maculata. All fungi belonged to the Russulaceae, an ectomycorrhizal family. Partitioning of Simpson’s diversity showed that 48% of the variance in occurrences of fungal species coincided with population boundaries in C. mertensiana, vs. 68% in C. maculata. This differentiation coincided with geography but not habitat in C. mertensiana. In contrast, likelihood ratio tests showed strong associations between fungal occurrence and both habitat and phenotype in C. maculata. For example, C. maculata populations growing under oaks had no fungi in common with nearby populations growing under conifers, and those above 2000 m had no fungi in common with those below 2000 m. However, plant genetic differentiation may underlie some of these patterns. C. mertensiana and C. maculata never shared fungal species, even when growing intermixed at the same site, demonstrating genetic control that was independent of habitat. Similarly, intermixed normal and pale‐coloured variants of C. maculata had no fungal species in common. These results demonstrate fine‐scale genetic influences and geographical mosaicism in a mycorrhizal interaction.

High specificity generally characterizes mycorrhizal association in rare lady's slipper orchids, genus Cypripedium

Ladys slipper orchids (Cypripedium spp.) are rare terrestrial plants that grow throughout the temperate Northern Hemisphere. Like all orchids, they require mycorrhizal fungi for germination and seedling nutrition. The nutritional relationships of adult Cypripedium mycorrhizae are unclear; however, Cypripedium distribution may be limited by mycorrhizal specificity, whether this specificity occurs only during the seedling stage or carries on into adulthood. We attempted to identify the primary mycorrhizal symbionts for 100 Cypripedium plants, and successfully did so with two Cypripedium calceolus, 10 Cypripedium californicum, six Cypripedium candidum, 16 Cypripedium fasciculatum, two Cypripedium guttatum, 12 Cypripedium montanum, and 11 Cypripedium parviflorum plants from a total of 44 populations in Europe and North America, yielding fungal nuclear large subunit and mitochondrial large subunit sequence and RFLP (restriction fragment length polymorphism) data for 59 plants. Because orchid mycorrhizal fungi are typically observed without fruiting structures, we assessed fungal identity through direct PCR (polymerase chain reaction) amplification of fungal genes from mycorrhizally colonized root tissue. Phylogenetic analysis revealed that the great majority of Cypripedium mycorrhizal fungi are members of narrow clades within the fungal family Tulasnellaceae. Rarely occurring root endophytes include members of the Sebacinaceae, Ceratobasidiaceae, and the ascomycetous genus, Phialophora. C. californicum was the only orchid species with apparently low specificity, as it associated with tulasnelloid, ceratobasidioid, and sebacinoid fungi in roughly equal proportion. Our results add support to the growing literature showing that high specificity is not limited to nonphotosynthetic plants, but also occurs in photosynthetic ones.

Divergence in mycorrhizal specialization within Hexalectris spicata (Orchidaceae), a nonphotosynthetic desert orchid

Evidence is accumulating for specialized yet evolutionarily dynamic associations between orchids and their mycorrhizal fungi. However, the frequency of tight mycorrhizal specificity and the phylogenetic scale of changes in specificity within the Orchidaceae are presently unknown. We used microscopic observations and PCR-based methods to address these questions in three taxa of nonphotosynthetic orchids within the Hexalectris spicata complex. Fungal ITS RFLP analysis and sequences of the ITS and nuclear LSU ribosomal gene fragments allowed us to identify the fungi colonizing 25 individuals and 50 roots. Thanatephorus ochraceus (Ceratobasidiaceae) was an occasional colonizer of mycorrhizal roots and nonmycorrhizal rhizomes. Members of the Sebacinaceae were the primary mycorrhizal fungi in every Hexalectris root and were phylogenetically intermixed with ectomycorrhizal taxa. These associates fell into six ITS RFLP types labeled B through G. Types B, C, D, and G were found in samples of H. spicata var. spicata, while only type E was found in H. spicata var. arizonica and only type F was found in H. revoluta. These results provide preliminary evidence for divergence in mycorrhizal specificity between these two closely related orchid taxa. We hypothesize that mycorrhizal interactions have contributed to the evolutionary diversification of the Orchidaceae.

Partner Choice in Nitrogen-Fixation Mutualisms of Legumes and Rhizobia

Abstract Mutualistic interactions are widespread and obligatory for many organisms, yet their evolutionary persistence in the face of cheating is theoretically puzzling. Nutrient-acquisition symbioses between plants and soil microbes are critically important to plant evolution and ecosystem function, yet we know almost nothing about the evolutionary dynamics and mechanisms of persistence of these ancient mutualisms. Partner-choice and partner-fidelity are mechanisms for dealing with cheaters, and can theoretically allow mutualisms to persist despite cheaters. Many models of cooperative behavior assume pairwise interactions, while most plant-microbe nutrient-acquisition symbioses involve a single plant interacting with numerous microbes. Market models, in contrast, are well suited to mutualisms in which single plants attempt to conduct mutually beneficial resource exchange with multiple individuals. Market models assume that one partner chooses to trade with a subset of individuals selected from a market of potential partners. Hence, determining whether partner-choice occurs in plant-microbe mutualisms is critical to understanding the evolutionary persistence and dynamics of these symbioses. The nitrogen-fixation/carbon-fixation mutualism between leguminous plants and rhizobial bacteria is widespread, ancient, and important for ecosystem function and human nutrition. It also involves single plants interacting simultaneously with several to many bacterial partners, including ineffective (“cheating”) strains. We review the existing literature and find that this mutualism displays several elements of partner-choice, and may match the requirements of the market paradigm. We conclude by identifying profitable questions for future research.

THE EVOLUTIONARY HISTORY OF MYCORRHIZAL SPECIFICITY AMONG LADY'S SLIPPER ORCHIDS

Abstract Although coevolution is acknowledged to occur in nature, coevolutionary patterns in symbioses not involving species-to-species relationships are poorly understood. Mycorrhizal plants are thought to be too generalist to coevolve with their symbiotic fungi; yet some plants, including some orchids, exhibit strikingly narrow mycorrhizal specificity. Here, we assess the evolutionary history of mycorrhizal specificity in the ladys slipper orchid genus, Cypripedium. We sampled 90 populations of 15 taxa across three continents, using DNA methods to identify fungal symbionts and quantify mycorrhizal specificity. We assessed phylogenetic relationships among sampled Cypripedium taxa, onto which we mapped mycorrhizal specificity. Cypripedium taxa associated almost exclusively with fungi within family Tulasnellaceae. Ancestral specificity appears to have been narrow, followed by a broadening after the divergence of C. debile. Specificity then narrowed, resulting in strikingly narrow specificity in most of the taxa in this study, with no taxon rewidening to the same extant as basal members of the genus. Sympatric taxa generally associated with different sets of fungi, and most clades of Cypripedium-mycorrhizal fungi were found throughout much of the northern hemisphere, suggesting that these evolutionary patterns in specificity are not the result of biogeographic lack of opportunity to associate with potential partners. Mycorrhizal specificity in genus Cypripedium appears to be an evolvable trait, and associations with particular fungi are phylogenetically conserved.