The functional role of ericoid mycorrhizal plants and fungi on carbon and nitrogen dynamics in forests.

Ericoid mycorrhizal (ErM) shrubs commonly occur in forest understories and could therefore alter arbuscular (AM) and/or ectomycorrhizal (EcM) tree effects on soil carbon and nitrogen dynamics. Specifically, ErM fungi have extensive organic matter decay capabilities, and ErM plant and fungal tissues have high concentrations of secondary compounds that can form persistent complexes in the soil. Together, these traits could contribute to organic matter accumulation and inorganic nutrient limitation. These effects could also differ in AM- vs EcM-dominated stands at multiple scales within and among forest biomes by, for instance, altering fungal guild interactions. Most work on ErM effects in forests has been conducted in boreal forests dominated by EcM trees. However, ErM plants occur in c. 96, 69 and 29% of boreal, temperate and tropical forests, respectively. Within tropical montane forests, the effects of ErM plants could be particularly pronounced because their traits are more distinct from AM than EcM trees. Because ErM fungi can function as free-living saprotrophs, they could also be more resilient to forest disturbances than obligate symbionts. Further consideration of ErM effects within and among forest biomes could improve our understanding of how cooccurring mycorrhizal types interact to collectively affect soil carbon and nitrogen dynamics under changing conditions.

Corrigendum: The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education.

[This corrects the article DOI: 10.1093/biosci/biz140.].

A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens.

PREMISE: Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS: We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS: Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS: Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.

Habitat quality and disturbance drive lichen species richness in a temperate biodiversity hotspot.

The impacts of disturbance on biodiversity and distributions have been studied in many systems. Yet, comparatively less is known about how lichens-obligate symbiotic organisms-respond to disturbance. Successful establishment and development of lichens require a minimum of two compatible yet usually unrelated species to be present in an environment, suggesting disturbance might be particularly detrimental. To address this gap, we focused on lichens, which are obligate symbiotic organisms that function as hubs of trophic interactions. Our investigation was conducted in the southern Appalachian Mountains, USA. We conducted complete biodiversity inventories of lichens (all growth forms, reproductive modes, substrates) across 47, 1-ha plots to test classic models of responses to disturbance (e.g., linear, unimodal). Disturbance was quantified in each plot using a standardized suite of habitat quality variables. We additionally quantified woody plant diversity, forest density, rock density, as well as environmental factors (elevation, temperature, precipitation, net primary productivity, slope, aspect) and analyzed their impacts on lichen biodiversity. Our analyses recovered a strong, positive, linear relationship between lichen biodiversity and habitat quality: lower levels of disturbance correlate to higher species diversity. With few exceptions, additional variables failed to significantly explain variation in diversity among plots for the 509 total lichen species, but we caution that total variation in some of these variables was limited in our study area. Strong, detrimental impacts of disturbance on lichen biodiversity raises concerns about conservation and land management practices that fail to incorporate complete estimates of biodiversity, especially from ecologically important organisms such as lichens.

Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses.

Symbioses among co-evolving taxa are often marked by genome reductions such as a loss of protein-coding genes in at least one of the partners as a means of reducing redundancy or intergenomic conflict. To explore this phenomenon in an iconic yet under-studied group of obligate symbiotic organisms, mitochondrial genomes of 22 newly sequenced and annotated species of lichenized fungi were compared to 167 mitochondrial genomes of nonlichenized fungi. Our results demonstrate the first broad-scale loss of atp9 from mitochondria of lichenized fungi. Despite key functions in mitochondrial energy production, we show that atp9 has been independently lost in three different lineages spanning 10 of the 22 studied species. A search for predicted, functional copies of atp9 among genomes of other symbionts involved in each lichen revealed the full-length, presumably functional copies of atp9 in either the photosynthetic algal partner or in other symbiotic fungi in all 10 instances. Together, these data yield evidence of an obligate symbiotic relationship in which core genomic processes have been streamlined, likely due to co-evolution.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

The Parmotrema acid test: a look at species delineation in the P. perforatum group 40 y later.

Parmotrema perforatum and its relatives form a morphologically distinctive group of species, most of which are common and endemic to eastern North America. Species delimitation in this ecologically important group was the subject of extensive inquiry before the advent of molecular systematics and computationally intensive niche modeling. As part of a large-scale lichen biodiversity inventory of the Mid-Atlantic Coastal Plain, we used ITS sequence data to examine the utility of characters (morphological, chemical, reproductive, ecological) in circumscribing four species in this group (P. hypoleucinum, P. hypotropum, P. perforatum, P. subrigidum). We found that P. hypoleucinum and P. subrigidum as currently circumscribed are monophyletic and the latter comprises two chemotypes differing in the presence or absence of norstictic acid in addition to alectoronic acid. The sequences of P. hypotropum and P. perforatum, which are chemically identical species and differ only in reproductive mode, were intermixed in a single, well-supported clade. The two chemotypes of P. subrigidum are partially allopatric and their sequences are >99% identical. Nonetheless, niche modeling suggests they occupy significantly different ecological niches. These results provide a new perspective on much-debated questions on species circumscription in lichens and suggest new avenues for genetic, ecological and systematic research.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).

• Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.• Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria.• Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes.• Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America.

Discovery of New Genomic Configuration of Mating-Type Loci in the Largest Lineage of Lichen-Forming Fungi.

The genetic architecture of mating-type loci in lichen-forming fungi has been characterized in very few taxa. Despite the limited data, and in contrast to all other major fungal lineages, arrangements that have both mating-type alleles in a single haploid genome have been hypothesized to be absent from the largest lineage of lichen-forming fungi, the Lecanoromycetes. We report the discovery of both mating-type alleles from the haploid genomes of three species within this group. Our results demonstrate that Lecanoromycetes are not an outlier among Ascomycetes.

Phylogeny of the genus Loxospora s.l. (Sarrameanales, Lecanoromycetes, Ascomycota), with Chicitaea gen. nov. and five new combinations in Chicitaea and Loxospora.

Loxospora is a genus of crustose lichens containing 13 accepted species that can be separated into two groups, based on differences in secondary chemistry that correlate with differences in characters of the sexual reproductive structures (asci and ascospores). Molecular phylogenetic analyses recovered these groups as monophyletic and support their recognition as distinct genera that differ in phenotypic characters. Species containing 2'-O-methylperlatolic acid are transferred to the new genus, Chicitaea Guzow-Krzem., Kukwa & Lendemer and four new combinations are proposed: C.assateaguensis (Lendemer) Guzow-Krzem., Kukwa & Lendemer, C.confusa (Lendemer) Guzow-Krzem., Kukwa & Lendemer, C.cristinae (Guzow-Krzem., Lubek, Kubiak & Kukwa) Guzow-Krzem., Kukwa & Lendemer and C.lecanoriformis (Lumbsch, A.W. Archer & Elix) Guzow-Krzem., Kukwa & Lendemer. The remaining species produce thamnolic acid and represent Loxospora s.str. Haplotype analyses recovered sequences of L.elatina in two distinct groups, one corresponding to L.elatina s.str. and one to Pertusariachloropolia, the latter being resurrected from synonymy of L.elatina and, thus, requiring the combination, L.chloropolia (Erichsen) Ptach-Styn, Guzow-Krzem., Tønsberg & Kukwa. Sequences of L.ochrophaea were found to be intermixed within the otherwise monophyletic L.elatina s.str. These two taxa, which differ in contrasting reproductive mode and overall geographic distributions, are maintained as distinct, pending further studies with additional molecular loci. Lectotypes are selected for Lecanoraelatina, Pertusariachloropolia and P.chloropoliaf.cana. The latter is a synonym of Loxosporachloropolia. New primers for the amplification of mtSSU are also presented.

A radical shift in the taxonomy of Lepraria s.l.: molecular and morphological studies shed new light on the evolution of asexuality and lichen growth form diversification.

A combination of molecular phylogenetic analyses of ITS and mtSSU sequences, morphological and chemical analyses were used to investigate the lineages nominally included in the sterile lichen genus Lepraria. A core group (Lepraria s. str.) was resolved as sister to Stereocaulon. Species producing the secondary compounds argopsin, pannarin and usnic acid were found to belong to other lineages of lichen-forming ascomycetes. Study of Leprocaulon revealed that all species, except the type, likely represent members of Lepraria s. str. that have evolved a fruticose growth form. The correct name for the type species of Leprocaulon is shown to be L. quisquiliare, not L. microscopicum, and the genus is redefined to include several species previously placed in Lepraria. Leprocaulon quisquiliare is also shown to comprise two morphologically convergent species. The name is lectotypified and epitypified on material from the type region (Germany) and its application restricted to Old World populations. New World populations of L. quisquiliare are described as L. americanum. Leprocaulon, in its revised sense, is recognized in a new family (Leprocaulaceae) and order (Leprocaulales) sister to the Caliciales and including the genus Halecania. A new genus of Pilocarpaceae, Nelsenium, is introduced to accommodate Lepraria usnica. The status of Lepraria ecorticata is discussed in the context of usnic acid-producing Lecanora species. These nomenclatural novelties are proposed: (i) transfers from Leprocaulon to Lepraria: Lepraria albicans comb. nov., L. arbuscula comb. nov., L. congestum comb. nov., L. gracilescens comb. nov., L. pseudoarbuscula comb. nov., L. subalbicans comb. nov., L. tenellum comb. nov.; (ii) transfers from Lepraria to Leprocaulon: Leprocaulon adhaerens comb. nov., L. coriense, L. santamonicae comb. nov., L. terricola comb. nov. and L. textum comb. nov.; (iii) new taxa: Leprocaulales ord. nov., Leprocaulaceae fam. nov., Nelsenium gen. nov., Leprocaulon americanum sp. nov. and L. knudsenii sp. nov.

Carbon-concentrating mechanisms are a key trait in lichen ecology and distribution.

Carbon-concentrating mechanisms (CCMs) are a widespread phenomenon in photosynthetic organisms. In vascular plants, the evolution of CCMs ([C44-carbon compound] and crassulacean acid metabolism [CAM]) is associated with significant shifts, most often to hot, dry and bright, or aquatic environments. If and how CCMs drive distributions of other terrestrial photosynthetic organisms, remains little studied. Lichens are ecologically important obligate symbioses between fungi and photosynthetic organisms. The primary photosynthetic partner in these symbioses can include CCM-presenting cyanobacteria (as carboxysomes), CCM-presenting green algae (as pyrenoids) or green algae lacking any CCM. We use an extensive dataset of lichen communities from eastern North America, spanning a wide climatic range, to test the importance of CCMs as predictors of lichen ecology and distribution. We show that the presence or absence of CCMs leads to opposite responses to temperature and precipitation in green algal lichens, and different responses in cyanobacterial lichens. These responses contrast with our understanding of lichen physiology, whereby CCMs mitigate carbon limitation by water saturation at the cost of efficient use of vapor hydration. This study demonstrates that CCM status is a key functional trait in obligate lichen symbioses, equivalent in importance to its role in vascular plants, and central for studying present and future climate responses.

Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales.

Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the "true" reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.

A call to reconceptualize lichen symbioses.

Several decades of research across disciplines have overturned historical perspectives of symbioses dominated by binary characterizations of highly specific species-species interactions. This paradigm shift has unlocked the previously underappreciated and overlooked dynamism of fungal mutualisms such as mycorrhizae. Lichens are another example of important fungal mutualisms where reconceptualization is urgently needed to realize their potential as model systems. This reconceptualization requires both an objective synthesis of new data and envisioning a revised integrative approach that unifies the spectrum of ecology and evolution. We propose a ten-theme framework that if pursued would propel lichens to the vanguard of symbiotic theory.

Unraveling usnic acid: a comparison of biosynthetic gene clusters between two reindeer lichen (Cladonia rangiferina and C. uncialis).

Lichenized fungi are known for their production of a diversity of secondary metabolites, many of which have broad biological and pharmacological applications. By far the most well-studied of these metabolites is usnic acid. While this metabolite has been well-known and researched for decades, the gene cluster responsible for its production was only recently identified from the species Cladonia uncialis. Usnic acid production varies considerably in the genus Cladonia, even among closely related taxa, and many species, such as C. rangiferina, have been inferred to be incapable of producing the metabolite based on analysis by thin-layer chromatography (TLC). We sequenced and examined the usnic acid biosynthetic gene clusters, or lack thereof, from four closely related Cladonia species (C. oricola, C. rangiferina, C. stygia, and C. subtenuis), and compare them against those of C. uncialis. We complement this comparison with tiered chemical profile analyses to confirm the presence or absence of usnic acid in select samples, using both HPLC and LC-MS. Despite long-standing reporting that C. rangiferina lacks the ability to produce usnic acid, we observed functional gene clusters from the species and detected usnic acid when extracts were examined by LC-MS. By contrast, C. stygia and C. oricola, have been previously described as lacking the ability to produce usnic acid, lacked the gene cluster entirely, and no usnic acid could be detected in C. oricola extracts via HPLC or LC-MS. This work suggests that chemical profiles attained through inexpensive and low-sensitivity methods like TLC may fail to detect low abundance metabolites that can be taxonomically informative. This study also bolsters understanding of the usnic acid gene cluster in lichens, revealing differences among domains of the polyketide synthase which may explain observed differences in expression. These results reinforce the need for comprehensive characterization of lichen secondary metabolite profiles with sensitive LC-MS methods.

A taxonomic revision of the North American species of Lepraria s.l. that produce divaricatic acid, with notes on the type species of the genus L. incana.

The divaricatic acid-producing populations of Lepraria in North America north of Mexico are revised with traditional morphological characters, chemistry, ecology, biogeography, and ITS1, 5.8S, and ITS2 sequence data. Three taxa are accepted: L. cryophila, L. hodkinsoniana sp. nov. and L. pacifica sp. nov. Both Lepraria crassissima and L. incana are excluded from the study area. Noncryptic, semicryptic and fully cryptic species concepts in Lepraria are discussed with emphasis on the practical integration of molecular characters into taxonomic frameworks based on non-molecular characters.

Chapter F of the International Code of Nomenclature for algae, fungi, and plants as approved by the 11th International Mycological Congress, San Juan, Puerto Rico, July 2018.

A revised version of Chapter F of the International Code of Nomenclature for algae, fungi, and plants is presented, incorporating amendments approved by the Fungal Nomenclature Session of the 11th International Mycological Congress held in San Juan, Puerto Rico in July 2018. The process leading to the amendments is outlined. Key changes in the San Juan Chapter F are (1) removal of option to use a colon to indicate the sanctioned status of a name, (2) introduction of correctability for incorrectly cited identifiers of names and typifications, and (3) introduction of option to use name identifiers in place of author citations. Examples have been added to aid the interpretation of new Articles and Recommendations, and Examples have also been added to the existing Art. F.3.7 concerning the protection extended to new combinations based on sanctioned names or basionyms of sanctioned names (which has been re-worded), and to Art. F.3.9 concerning typification of names accepted in the sanctioning works.