Adobe® Photoshop® CS3 Extended software and a photographic time series were used to generate accurate and precise measures of change in the area, perimeter and diameter of Rhizocarpon thalli at one, three and seven year intervals. Systematic measurements at a fixed grid of eight diameters per thallus showed a rapid and highly variable diametric growth phase in the smallest thalli (<5 mm2) and slower diametric growth (<0·01 mm2 yr–1) in larger thalli (5–500 mm2). When standardized to an annual rate, the areal growth trend was similar, regardless of the number of years studied. This suggests that the areal and diametric growth of small and mid-sized Rhizocarpon thalli may be insensitive to annual climatic variation and can be accurately characterized by repeat measurements taken over months rather than decades. Unlike diametric growth rate, change in thallus area and perimeter are statistically robust measures of growth in Rhizocarpon thalli. Our mean measurement accuracy was 99%. Measurement precision (reproducibility) was >95% (P>0·05) for thallus area and >96% for thallus perimeter. Our technique is tedious, but on flat rocks it can resolve and accurately measure change in thallus morphology at the sub-millimeter scale, and it can be used with recent and/or historical images.

It has been suggested that the absence of anthraquinones is not a synapomorphic character, but appears independently in unrelated lineages of Teloschistaceae. We analyzed ITS nrDNA regions in species of the genus Caloplaca and present evidence for five such examples: the Caloplaca cerina group, C. obscurella, the C. servitiana group, the C. xerica group and the C. variabilis group (Pyrenodesmia). In some cases, loss of anthraquinones is observed only in individuals within ordinarily pigmented populations, but sometimes the loss covers whole lineages containing one or more species. Both situations are observed in the C. servitiana group. Loss of anthraquinones is always followed by the synthesis of ‘alternative’ pigments (often Sedifolia-grey). In the specimens with anthraquinone-containing apothecia studied, these pigments are not visible in apothecial sections after dissolving anthraquinones in K. Fully unpigmented apothecia have not been observed.

The Caloplaca xerica group is a newly established, infraspecific grouping of species related to, and similar to, C. xerica. The Caloplaca servitiana group is also newly established and represents an isolated lineage covering two rather different, but related species. Caloplaca neotaurica is described here as a new species with apothecia of two colour variants; orange-red (with anthraquinones) and grey (with Sedifolia-grey).

The genus Huea represents another taxon lacking anthraquinones within Teloschistaceae. The genera Apatoplaca and Cephalophysis, which lack anthraquinones, are tentatively placed in Teloschistaceae, but their phylogenetic identity has not been recognized. Hueidea is reported to have no anthraquinones, but its secondary metabolites should be studied further and its possible placement in Teloschistaceae assessed.

We suggest that Caloplaca abbreviata var. lecideoides and C. celata represent variants of C. stillicidiorum lacking anthraquinones.

It has recently been discovered that lichens contain a serine protease capable of degrading the pathogenic prion protein, the etiological agent of prion diseases such as sheep scrapie and cervid chronic wasting disease. Limited methods are available to degrade or inactivate prion disease agents, especially in the environment, and lichens or their serine protease could prove important for management of these diseases. Scant information is available regarding the presence or absence of the protease responsible for degrading prion protein (PrP) in lichen species and, in this study, we tested the hypothesis that PrP degradation activity in lichens is phylogenetically-based by testing 44 species of Cladonia lichens, a genus for which a significant portion of the phylogeny is well established. We categorized PrP degradation activity among the 44 species (high, moderate, low or none) and found that activity in Cladonia species did not correspond with phylogenetic position of the species. Degradation of PrP did correspond, however, with three classical taxonomic characters within the genus: species with brown apothecia, no usnic acid, and the presence of a cortex. Of the 44 species studied, 18 (41%) had either high or moderate PrP degradation activity, suggesting the protease may be frequent in this genus of lichens.

The type collection of Parmelia goebelii (Bulbothrix goebelii) was discovered to be a mixture of several different Bulbothrix species. The true identity of B. goebelii is established and problems regarding the variability of this species discussed. The species B. papyrina, B. scortella and B. subdissecta, synonymized with B. goebelii by Hale, are resurrected as valid taxa. A detailed description of B. goebelii is presented, its lectotype is selected, and the characteristics of all four species discussed.

In our earlier work, we demonstrated the presence of the multicopper oxidases tyrosinase and laccase in the cell walls of lichens from the Peltigerales, while these enzymes appeared to be absent in lichens from other orders. Likely roles for tyrosinase in lichens include melanin synthesis, the generation of quinones needed for laccase-mediated redox cycling, and the removal of harmful reactive molecules formed by this cycling. Non-Peltigeralean lichens will not need tyrosinase to detoxify laccase-generated radicals. However, many non-Peltigeralean lichens are often heavily melanized. Apparent absence of tyrosinase activity in these species prompted us to suggest that, in these lichens, melanins are probably synthesized by the polyketide pathway, which does not involve tyrosinase. Here, we surveyed intracellular tyrosinase activity in thallus homogenates from a range of lichens. Results showed that Peltigeralean species generally have much higher activities than species from other orders. However, the non-Peltigeralean lichen Dermatocarpon miniatum displays significant tyrosinase activity. In D. miniatum, tyrosinase differs from the corresponding enzyme from Peltigeralean lichens with respect to cellular location, substratum specificity, stability and pH optimum. Furthermore, unlike Peltigeralean lichens, in D. miniatum tyrosinase activity increased strongly following the rehydration of dry thalli. These differences are possibly a consequence of the role of tyrosinase in melanin synthesis rather than laccase-mediated redox cycling.

A strain of the lichen mycobiont of Caloplaca erythrantha, isolated from ascospores, was cultured axenically on different solid media. Four of the media employed supported the development of colonies and production of the two major lichen secondary metabolites. These media were: BMYE (mannitol 2%, yeast extract 0·1%, in Bold's basal medium); MEYE (malt extract 2%, yeast extract 0·2%, in distilled water); Hamada's MY10 (malt extract 1%, yeast extract 0·4%, sucrose 10%, in distilled water); and the new BMRM (Bold mannitol rich medium, mannitol 5·3%, malt extract 1%, yeast extract 0·4% in Bold's mineral medium). Percentages refer to final medium volume. The fungal colonies developed well on the four media and produced emodin and 7-chloroemodin, the major secondary compounds of the lichen apothecia. Crystals deposited richly on the external surface of the hyphae, as observed with an optical microscope. The two anthraquinones were purified from the lichen thallus, apothecia and cultured mycelia, and identified by chromatographic (TLC, HPLC) and spectroscopic (NMR, MS) methods. The analysis of lichen apothecia revealed the presence of emodin (0·90% w/w) and 7-chloroemodin (0·56% w/w), whereas colonies cultured for five months generally produced higher percentages than the lichen: 1·72% emodin and 0·30% 7-chloroemodin on BMYE; 0·21% and 0·95% on MEYE; 7·82% and 7·48% on MY10; and 11·70% and 10·80% on BMRM. These results show that the production of both anthraquinones was promoted significantly in mycobiont cultures with high concentrations of the carbon sources sucrose or mannitol, with a higher effect being observed with the latter.

To investigate the association between, and the reproductive modes of, mycobiont and photobiont in the lichen Parmotrema tinctorum, microsatellite markers (SSR markers) were developed for both bionts and genotypic analysis was performed for thalli in a Pinus thunbergii forest. In a within-thallus analysis, tissue pieces were sampled from many portions within each of five thalli. Within-thallus variation for both mycobiont and photobiont differed among the thalli investigated, suggesting that a single thallus can be derived from either a single mycobiont origin with or without occasional changes in the photobiont, or fusion of several independent thalli. In the within-tree analysis, thalli with the same genotypes were found on individual trees, suggesting the presence of short-distance isidium dispersal. In the within-stand analysis, genotypically similar photobionts tended to be associated with the same mycobiont genotype, suggesting the participation of local dispersal via isidia. The overall index of association (IA) for the mycobiont in the stand probably indicates the dominance of sexual reproduction, in contrast to that of the photobiont, where dominance of asexual reproduction is suggested. IA's of mycobiont and photobiont were also calculated for thalli collected from larger areas, where there is a signature for sexual reproduction for photobiont.

Although several lichen inventories exist for European ultramafic sites, only four surveys of serpentine lichens for North America have been published to date. Of those, only one has been conducted in California. We conducted a survey of saxicolous lichens from ultramafic rocks (including nephrite, partially serpentinized peridotite, and serpentinite) and non-ultramafic rocks (including silica-carbonate, shale, and sandstone) at the New Idria serpentinite mass, San Benito County, California. X-ray Fluorescence Analysis of the rocks from which the lichens were collected revealed significant elemental differences between the ultramafic and non-ultramafic rocks for 26 of the 32 major and trace elements analyzed. We identified a total of 119 species of lichenized and lichenicolous fungi; 60 species were restricted to ultramafic substrata, 19 to silica-carbonate, and 15 to shale and sandstone. Only 4 species were shared in common. A permutational multivariate analysis of variance (perMANOVA) test revealed significant differences in lichen assemblages between ultramafic and non-ultramafic rocks at the species level but not at the generic level, with species richness (alpha-diversity) significantly greater at the ultramafic sites. We suggest that, although differences in geochemistry clearly influence the lichen community composition, other factors, especially substratum age and the physical characteristics of the rock, are of equal, if not greater, importance. Of all the species collected, six, Buellia aethalea, B. ocellata, Caloplaca oblongula, Rhizocarpon saurinum, Thelocarpon laureri, and Trapelia obtegens, are reported new to California, along with an apparently previously undescribed Solenopsora sp. The rest of the species encountered are relatively frequent in the lichen flora of southern and central California, except Aspicilia praecrenata, a rare California endemic that we collected on both ultramafic and non-ultramafic rocks.

Lichens are a fascinating example of a symbiotic mutualism. It is still uncertain which processes guide fungal-photobiont interactions, and whether they are random or of a more complex nature. Here, the fungal-algal interactions in Ramalina menziesii and co-occurring taxa are analyzed by using DNA sequences of the algal Internal Transcribed Spacer region (ITS), to investigate fungal-algal associations in juvenile R. menziesii and allied species. Algal species were identified by a combination of BLAST searches, median-joining network analysis, and Bayesian phylogenetics. Fungal-algal networks were analyzed for nestedness, both at the species and haplotype level (fungal species vs. algal haplotypes), and the networks were inspected for evidence of compartmentalization. Bayesian phylogenetic trees indicated that the widespread green alga Trebouxia decolorans associated with R. menziesii, as well as six other fungal species. Four additional fungal species interacted with four different species of Trebouxia. Only in one out of ten samples were algal haplotypes shared with the nearest neighbours of juvenile R. menziesii. Fungal-algal species interactions were compartmentalized, while at the level of algal haplotypes, nestedness was found. This pattern is similar to the compartmentalization found in other intimately interacting mutualists.