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Bacterial symbionts are essential components of healthy biological systems. They are increasingly recognized as important factors in the study and management of threatened species and ecosystems. Despite management shifts at the ecosystem level, microbial communities are often neglected in discussions of holobiont conservation in favor of the primary members of a symbiosis. In this study, we addressed the bacterial community knowledge gap for one of two federally endangered lichen species in the United States, Cetradonia linearis (Cladoniaceae). We collected 28 samples of the endangered rock gnome lichen (Cetradonia linearis) from 13 sites and characterized bacterial communities in thalli using 16S rRNA metabarcoding to investigate the factors influencing the microbiome composition and diversity within the thallus. We found that Proteobacteria (37.8% ± 10.3) and Acidobacteria (25.9% ± 6.0) were the most abundant phyla recovered. Cyanobacteria were a major component of the microbiome in some individuals, despite this species associating with a green algal symbiont. Habitat, climate, and geography were all found to have significant influences on bacterial community composition. An analysis of the core microbiome at a 90% threshold revealed shared amplicon sequence variants in the microbiomes of other lichens in the family Cladoniaceae. We concluded that the bacterial microbiome of Cetradonia linearis is influenced by environmental factors and that some bacterial taxa may be core to this group. Further exploration into the microbiomes of rare lichen species is needed to understand the importance of bacterial symbionts to lichen diversity and distributions. 

This course-based undergraduate research experience (CURE) focuses on developing hypotheses about how traits influence the range sizes of species. Topics with substantive content include symbioses, the Appalachian Mountains, lichen morphology, and natural history collections. Scientific skills development modules focus on hypothesis development and testing, geographic information systems, statistics, and preparing presentations and manuscripts. The CURE leverages a large-scale digitized set of freely available images of lichen herbarium specimens. It can be implemented in in-person, online, or hybrid classrooms and only requires students have access to a computer and the internet. 

Thirty years after its designation as a federally endangered species, the Florida Perforate Cladonia (FPC) remains imperiled in isolated populations in the Florida scrub in the southeastern USA. For threatened and endangered species, such as FPC, reference genomes provide critical insight into genomic diversity, local adaptations, landscape-level genetics, and phylogenomics. Using high-throughput sequencing, we assemble the first draft nuclear and mitochondrial genomes for the FPC mycobiont—Cladonia perforata. We also assess genetic diversity within and among populations in southeastern Florida using genome-scale data and investigate diversity across the entire nuclear ribosomal cistron, including the standard DNA barcoding marker for fungi. The draft nuclear genome spanned 33.6 Mb, and the complete, circular mitochondrial genome was 59 Kb. We also generated the first chloroplast genome, to our knowledge, for the photobiont genus associated with FPC, an undescribed Asterochloris species. We inferred the presence of multiple, distinct mycobiont parental genotypes (genets) occurring at local scales in southeastern Florida, and strikingly, no genets were shared among even the closest sample sites. All sampled thalli shared identical mitochondrial genomes, while the nuclear ribosomal cistron showed limited variability—highlighting the genetic resolution provided by nuclear genome-scale datasets. The genomic resources generated here provide critical resources for informed conservation efforts for the FPC. 

Abstract Complete chromosomal-level assemblies of fungal genomes are rare. The intimate ecological symbioses and complex reproduction strategies utilized by fungi make highly contiguous, gapless genome assemblies particularly difficult. Here, we use long-read sequencing on the Oxford Nanopore Technology MinION platform to sequence and assemble the genome of Lepraria neglecta ( Ascomycota , Lecanorales ). In addition to eight contigs ascribable to chromosomes, six of which are assembled telomere-to-telomere, we discovered the presence of a complete MAT locus with two conserved MAT1-2 genes and a putative MAT1-1 pseudogene. The full genome assembly of a widespread, common species presents an opportunity for new insights into lichen reproduction while the presence of the mating-type locus in the genome of an asexual lichen raises fundamental questions about reproductive biology in fungi generally. 

Community science-generated biodiversity data can provide essential information for understanding species distributions, behaviors and conservation statuses. However, their utility can be limited due to high uncertainty and variability in quality, especially for small taxonomically difficult organisms like fungi and insects. One important set of community-generated data that are increasingly used by scientists are Research Grade (RG) iNaturalist observations. These observations are aggregated into the Global Biodiversity Information Facility database. Here we assessed the accuracy of RG lichen observations in iNaturalist. Lichens are mutualistic symbioses formed between fungi and a photosynthetic partner, either algae or cyanobacteria that occur in every terrestrial ecosystem on the planet (Brodo et al. 2001). They are sensitive indicators of environmental health, especially air quality, and provide essental food and nesting material for animals, along with performing many other ecosystem services (Allen and Lendemer 2021, Brodo et al. 2001, Nimis et al. 2002). We examined hundreds of observations and determined if the identification was correct, if it was not possible to identify the observation given the data provided, or if the identification was incorrect. Identification accuracy of selected species varied widely, from zero observations with enough information for correct identification (e.g., Rhizocarpon geographicum and Cladonia chlorophaea ) to 100% correct identifications (e.g., Cetradonia linearis and Physconia subpallida , McMullin and Allen 2022). Most frequently, species that require microscopic examination or chemical tests for accurate identification were unable to be verified versus those that require only macromorphology. We provide a series of suggestions for best practices to improve the quality of RG observations and thus the utility of community-generated observation data for taxonomically difficult organisms. 

We assess the identification accuracy of ‘research grade’ observations of lichens posted on the online platform iNaturalist. Our results show that these observations are frequently misidentified or lack the necessary chemical and (or) microscopic information for accurate identification. Lichens are a taxonomically difficult group, but they are ubiquitous and eye-catching and are regularly the subject of observations posted on iNaturalist. Therefore, we provide best practice recommendations for posting lichen observations and commenting on observations. Data from iNaturalist are a valuable tool for understanding and managing biodiversity, particularly at this crucial time when large scale biodiversity decline is occurring globally. However, the data must be accurate for them to effectively support biodiversity conservation efforts. Our recommendations are also applicable to other taxonomically difficult taxa. 

ABSTRACT The draft genome sequence of Bacidia gigantensis , a lichenized fungus in the order Lecanorales, was sequenced directly from a herbarium specimen collected from the type locality at Sleeping Giant Provincial Park in Ontario, Canada. Using long-read sequencing on the Oxford Nanopore PromethION platform, we assembled a nearly complete genome sequence.