New lichen records from the Novgorod Region, Russia

Twenty lichen species are reported as new to the Novgorod Region (Russia) from Valdaysky National Park and Rdeysky Nature Reserve. Pyrenula chlorospila is recorded for the first time for European Russia outside Caucasus. Acrocordia cavata, Pertusaria coccodes, Rostania occultata and Scytinium subtile are recommended to be included in the Red Data Book of the Novgorod Region.

New records of lichens and allied fungi from the Leningrad Region, Russia. V

Eight species of lichens and seven lichenicolous fungi are reported from the Leningrad Region. Agonimia repleta, Protoparmelia hypotremella and Stereocaulon taeniarum are reported for the first time for Russia; Clypeococcum cetrariae is new to the European Russia; Lepraria nivalis, Merismatium aff. nigritellum (on Physcia aipolia) and Stigmidium leprariae are new to the North-Western European Russia; Cladonia macroceras, C. strepsilis, Endococcus fusiger, Lichenoconium erodens, Lobothallia melanaspis, Niesslia cladoniicola and Skyttella mulleri are new to the Leningrad Region; Sclerophora coniophaea is new to Saint Petersburg. The most noteworthy records are briefly discussed.

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae

New records of lichens and allied fungi from the Leningrad Region, Russia. VI

Eighteen species of lichens and five lichenicolous fungi are reported here for the Leningrad Region or Saint Petersburg. Of them, the lichens Absconditella delutula, Calogaya pusilla, Flavoplaca flavocitrina and Rinodina colobina are new for the North-Western European Russia, and the lichenicolous species Abrothallus parmeliarum, Diploschistes muscorum, Lichenochora cf. polycoccoides and Nieslia peltigericola – for the Leningrad Region; Cladonia novochlorophaea and Lichenodiplis lecanorae are reported for the first time for Saint Petersburg. The most noteworthy records are briefly discussed

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous “orphan” ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi

Phylogenomic tree of Rhizobiales bacteria

Supplementary file associated with Tagirdzhanova et al. 2023. A global survey of lichen symbionts from metagenomes Maximum likelihood phylogenetic tree of Rhizobiales.  The tree includes published genomes of Rhizobiales and Rhizobiales MAGs derived from lichen metagenomes (indicated in red). We generated the alignment of 120 marker genes using GTDB-Tk, and calculated the tree using IQ-TREE.   Includes two files:  1. rhizobiales.contree: treefile in Newick format 2. rhizobiales_annotated_tree.svg: annotated tree showing the taxonomic assignments of the genomes and presence/absence of genes related to nitrogen fixing and C1 metabolism</p

Phylogenomic trees of MAGs isolated from lichen metagenomes

Supplementary files associated with Tagirdzhanova et al. 2023. A global survey of lichen symbionts from metagenomes Maximum likelihood phylogenetic trees of the MAGs isolated from lichen metagenomes.  Includes three files:  1. bacterial.treefile  This tree was calculated using IQ-TREE and are based on alignments of marker genes (for prokaryotes: 120 marker genes from GTDB-Tk). 2. fungal.treefile 3. algal.treefile These two trees were calculated using the Phylociraptor pipeline. The trees were based on 1296 genes in algae and 709 genes in fungi. Concatenated phylogenies were calculated using IQ-TREE</p

The coming golden age for lichen biology

Lichens are a diverse group of organisms. They are both commonly observed but also mysterious. It has long been known that lichens are composite symbiotic associations of at least one fungus and an algal or cyanobacterial partner, but recent evidence suggests that they may be much more complex. We now know that there can be many constituent microorganisms in a lichen, organized into reproducible patterns that suggest a sophisticated communication and interplay between symbionts. We feel the time is right for a more concerted effort to understand lichen biology. Rapid advances in comparative genomics and metatranscriptomic approaches, coupled with recent breakthroughs in gene functional studies, suggest that lichens may now be more tractable to detailed analysis. Here we set out some of the big questions in lichen biology, and we speculate about the types of gene functions that may be critical to their development, as well as the molecular events that may lead to initial lichen formation. We define both the challenges and opportunities in lichen biology and offer a call to arms to study this remarkable group of organisms

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Abstract Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae

3D biofilms : in search of the polysaccharides holding together lichen symbioses

Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes