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''Cladonia grayi'', commonly known as Gray's cup lichen or Gray's pixie cup, is a species of
fruticose lichen A fruticose lichen is a form of lichen fungi that is characterized by a coral-like shrubby or bushy growth structure. It is formed from a symbiotic relationship of a photobiont such as green algae or less commonly cyanobacteria and one, two or m ...
in the family
Cladoniaceae The Cladoniaceae are a family of lichen-forming fungi in the order Lecanorales, comprising about 560 species distributed amongst 18 genera. This family is one of the largest among lichen-forming fungi and is globally distributed, from Arctic t ...
. It is characterised by small, leaf-like forming its and distinctive upright
podetia A podetium (plural: podetia) is the upright secondary thallus in ''Cladonia'' lichens. It is a hollow stalk extending from the . Podetia can be pointed stalks, club like, cupped, or branched in shape and may or may not contain the ascocarp, the f ...
(5–15 mm tall) that develop into goblet-shaped cups. The species contains several unique
lichen substance Lichen products, also known as lichen substances, are organic compounds produced by a lichen. Specifically, they are secondary metabolites. Lichen products are represented in several different chemical classes, including terpenoids, orcinol deri ...
s, primarily grayanic acid, which causes it to glow light blue under
ultraviolet light Ultraviolet radiation, also known as simply UV, is electromagnetic radiation of wavelengths of 10–400 nanometers, shorter than that of visible light, but longer than X-rays. UV radiation is present in sunlight and constitutes about 10% of th ...
, and has also been found to produce protective pyrrolopyrazine compounds. Its is the
green alga The green algae (: green alga) are a group of chlorophyll-containing autotrophic eukaryotes consisting of the phylum Prasinodermophyta and its unnamed sister group that contains the Chlorophyta and Charophyta/ Streptophyta. The land plants ( ...
l species '' Asterochloris glomerata''. The fungal component shows distinctive growth responses during development that occur only when encountering compatible algal cells, with the fungus growing extremely slowly at ≤1 cm per year in
culture Culture ( ) is a concept that encompasses the social behavior, institutions, and Social norm, norms found in human societies, as well as the knowledge, beliefs, arts, laws, Social norm, customs, capabilities, Attitude (psychology), attitudes ...
. Though found worldwide, ''C. grayi'' is most abundant in Arctic and
temperate In geography, the temperate climates of Earth occur in the middle latitudes (approximately 23.5° to 66.5° N/S of the Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ran ...
regions of the Northern Hemisphere. It typically grows on acidic including rotting wood, organic soil layers, and bare ground, showing particular abundance in
pine A pine is any conifer tree or shrub in the genus ''Pinus'' () of the family Pinaceae. ''Pinus'' is the sole genus in the subfamily Pinoideae. ''World Flora Online'' accepts 134 species-rank taxa (119 species and 15 nothospecies) of pines as cu ...
forests across a range of humidity conditions. Two chemical variants (chemotypes) have been documented: one containing only grayanic acid and 4-''O''-demethylgrayanic acid, and another that additionally contains substances of the
fumarprotocetraric acid Fumarprotocetraric acid is a chemical compound with the chemical formula . It is a secondary metabolite produced by a variety of lichens. Occurrence Fumarprotocetraric acid is mainly known for its occurrence in Iceland moss (''Cetraria islandica ...
complex.


Taxonomy

The
type specimen In biology, a type is a particular wikt:en:specimen, specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally associated. In other words, a type is an example that serves to ancho ...
of ''Cladonia grayi'' was collected in 1928 near Long Creek in Charlotte,
Mecklenburg County, North Carolina Mecklenburg County () is a County (United States), county located in the southwestern region of the U.S. state of North Carolina, in the United States. As of the 2020 United States census, 2020 census, the population was 1,115,482, making it th ...
(originally cited as "North Virginia"). It was distributed as part of Sandstede's ''Cladoniae Exsiccatae'' collection, number 1847. The
lectotype In biology, a type is a particular specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally associated. In other words, a type is an example that serves to anchor or centralizes ...
specimen is housed at the
Farlow Herbarium The Farlow Herbarium of Cryptogamic Botany is an herbarium and library at Harvard University with about 1,400,000 specimens, including approximately 75,000 types, of lichens, fungi, bryophytes, diatoms, and algae.Farlow Herbarium, Harvard Univers ...
(FH) at
Harvard University Harvard University is a Private university, private Ivy League research university in Cambridge, Massachusetts, United States. Founded in 1636 and named for its first benefactor, the History of the Puritans in North America, Puritan clergyma ...
and was designated by
Teuvo Ahti Teuvo "Ted" Tapio Ahti (born 14 June 1934) is a Finnish botanist and lichenologist who has made significant contributions to the taxonomy and biogeography of lichens. Known particularly for his work on the lichen family Cladoniaceae, he has h ...
in 1993 in his work published in ''Regnum Vegetabile''. Several forms of this species have been proposed, but it is unclear if these historical infrataxa have independent taxonomic significance. As Evans noted about form ''simplex'', "the present form may represent either a stage in the development of one of the more complex forms or a definitely arrested conditions which will not develop further." :*''C. grayi'' f. ''aberrans'' :*''C. grayi'' f. ''carpophora'' ::*A fertile form with abundant large brown apothecia on cup margins or stalks, characterized by dark grayish-green to olive-green podetia lacking squamules. :*''C. grayi'' f. ''centralis'' :*''C. grayi'' f. ''cyathiformis'' :*''C. grayi'' f. ''fasciculata'' :*''C. grayi'' f. ''grayi'' :*''C. grayi'' f. ''lacerata'' :*''C. grayi'' f. ''peritheta'' :*''C. grayi'' f. ''prolifera'' ::*A sterile form with unsquamulose podetia bearing scattered cup-like proliferations. :*''C. grayi'' f. ''simplex'' ::*A sterile form with simple, unsquamulose podetia having entire or nearly entire cup margins. :*''C. grayi'' f. ''squamulosa''
Common name In biology, a common name of a taxon or organism (also known as a vernacular name, English name, colloquial name, country name, popular name, or farmer's name) is a name that is based on the normal language of everyday life; and is often con ...
s that have been used for ''Cladonia grayi'' include "Gray's cup lichen" and "Gray's pixie cup".


Description

''Cladonia grayi'' is characterised by two main parts: a consisting of small, persistent leaf-like structures (), and a secondary thallus comprising upright stalks called
podetia A podetium (plural: podetia) is the upright secondary thallus in ''Cladonia'' lichens. It is a hollow stalk extending from the . Podetia can be pointed stalks, club like, cupped, or branched in shape and may or may not contain the ascocarp, the f ...
. The squamules, which form a crusty layer on the , are small (1 mm long and 1–2 mm wide) with wavy edges and tend to grow upward. The podetia, which are the most distinctive feature of the species, grow 5–15 mm tall and 2–7 mm wide. They are shaped like goblets () with long, narrow stalks expanding into round, globe-like cups at the top. These structures are typically light greyish-green but can appear dark or somewhat brownish. The surface of the podetia is covered with a protective layer () that can be bumpy and may peel off in patches as the lichen ages. The upper portions develop powdery areas (
soralia Soredia are common reproductive structures of lichens. Lichens reproduce asexually by employing simple fragmentation and production of soredia and isidia. Soredia are powdery propagules composed of fungal hyphae wrapped around cyanobacteria or g ...
) and measuring 40–130 
micrometre The micrometre (English in the Commonwealth of Nations, Commonwealth English as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer (American English), also commonly known by the non-SI term micron, is a uni ...
s in diameter, or they may produce small flaking squamules. The granules are thought to play a play in propagation of the species. The species' reproductive structures include dark brown spore-producing (
apothecia An ascocarp, or ascoma (: ascomata), is the fruiting body ( sporocarp) of an ascomycete phylum fungus. It consists of very tightly interwoven hyphae and millions of embedded asci, each of which typically contains four to eight ascospores. As ...
) that appear uncommonly along the cup margins, and more frequent smaller structures called
pycnidia A pycnidium (plural pycnidia) is an asexual fruiting body produced by mitosporic fungi, for instance in the order Sphaeropsidales ( Deuteromycota, Coelomycetes) or order Pleosporales (Ascomycota, Dothideomycetes). It is often spherical or inve ...
that produce a clear fluid.


Ultrastructure

When examined at a microscopic level, the fungal cells of ''C. grayi'' show several distinctive features. They contain nuclei with prominent pores, dense
cytoplasm The cytoplasm describes all the material within a eukaryotic or prokaryotic cell, enclosed by the cell membrane, including the organelles and excluding the nucleus in eukaryotic cells. The material inside the nucleus of a eukaryotic cell a ...
ic material, and storage areas for
glycogen Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. It is the main storage form of glucose in the human body. Glycogen functions as one of three regularly used forms ...
(a form of sugar). The cells also have specialised compartments called
vacuole A vacuole () is a membrane-bound organelle which is present in Plant cell, plant and Fungus, fungal Cell (biology), cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water ...
s that contain granular material, as well as
lipid Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...
bodies for fat storage. A particularly notable feature is that the fungal cell walls are covered with tiny thread-like projections called fibrils, which extend outward. When fungal cells grow close to each other, these fibrils can interconnect to form meshwork patterns, helping to bind the cells together. The fungus can also form unique supportive structures called "acellular struts." These struts appear to be modified branches that have lost their internal cellular contents but maintain their outer walls, and they may help provide structural support to the lichen body. These struts are more commonly found in parts of the fungus growing above the surface rather than those in direct contact with the growing surface.


Chemistry

When tested with standard chemical spot tests used in lichen identification, ''C. grayi'' shows distinctive reactions, particularly glowing ice-blue under
ultraviolet light Ultraviolet radiation, also known as simply UV, is electromagnetic radiation of wavelengths of 10–400 nanometers, shorter than that of visible light, but longer than X-rays. UV radiation is present in sunlight and constitutes about 10% of th ...
. It contains several unique lichen substances, primarily grayanic acid, with varying amounts of congrayanic and demethylgrayanic acids, and occasionally traces of
fumarprotocetraric acid Fumarprotocetraric acid is a chemical compound with the chemical formula . It is a secondary metabolite produced by a variety of lichens. Occurrence Fumarprotocetraric acid is mainly known for its occurrence in Iceland moss (''Cetraria islandica ...
complex. Grayanic acid, an
orcinol Orcinol is an organic compound with the formula CH3C6H3(OH)2. It occurs in many species of lichens including ''Roccella tinctoria'' and ''Lecanora''. Orcinol has been detected in the "toxic glue" of the ant species ''Camponotus saundersi''. It is ...
depsidone Depsidones (+ " depside" + "one") are chemical compounds that are sometimes found as secondary metabolites in lichens. They are esters that are both depsides and cyclic ethers. An example is norstictic acid Norstictic acid is a depsidone produ ...
, is a rare metabolite that has only been reported from ''
Neophyllis melacarpa ''Neophyllis'' a small genus of lichen-forming fungi in the family Sphaerophoraceae. The genus is endemic to Australasia, occurring in southeastern Australia, Tasmania and New Zealand. It comprises two recognised species characterised by small, ...
'' and ''C. grayi''. The thalli of ''C. grayi'' contain a diverse array of
carotenoid Carotenoids () are yellow, orange, and red organic pigments that are produced by plants and algae, as well as several bacteria, archaea, and fungi. Carotenoids give the characteristic color to pumpkins, carrots, parsnips, corn, tomatoes, cana ...
pigments, including β-carotene, α-carotene, β-cryptoxanthin,
zeaxanthin Zeaxanthin is one of the most common carotenoids in nature, and is used in the xanthophyll cycle. Synthesized in plants and some micro-organisms, it is the pigment that gives paprika (made from bell peppers), corn, saffron, goji ( wolfberries) ...
,
lutein Lutein (;"Lutein"
antheraxanthin Antheraxanthin (from ''ánthos'', Greek for "flower" and ''xanthos'', Greek for "yellow") is a bright yellow accessory pigment found in many organisms that perform photosynthesis. It is a xanthophyll cycle pigment, an oil-soluble alcohol within th ...
, hydroxyechinenone,
canthaxanthin Canthaxanthin is a keto-carotenoid pigment widely distributed in nature. Carotenoids belong to a larger class of phytochemicals known as terpenoids. The chemical formula of canthaxanthin is C40H52O2. It was first isolated in edible mushrooms. It ...
,
astaxanthin Astaxanthin is a keto- carotenoid within a group of chemical compounds known as carotenoids or terpenes. Astaxanthin is a metabolite of zeaxanthin and canthaxanthin, containing both hydroxyl and ketone functional groups. It is a lipid-solu ...
,
violaxanthin Violaxanthin is a xanthophyll pigment with an orange color found in a variety of plants. Violaxanthin is the product of the epoxidation of zeaxanthin where the oxygen atoms are from reactive oxygen species (ROS). Such ROS's arise when a plant i ...
, mutatoxanthin,
neoxanthin Neoxanthin is a carotenoid and xanthophyll. In plants, it is an intermediate in the biosynthesis of the plant hormone abscisic acid. It is often present in two forms: all-trans and 9-cis isomers. It is produced from violaxanthin, but a suspecte ...
and capsochrome. The concentrations and ratios of these carotenoids vary depending on light exposure, with specimens from more shaded environments showing higher total carotenoid content. In particular, lutein and violaxanthin are found in higher concentrations in shade-grown specimens, while zeaxanthin and antheraxanthin increase in specimens exposed to higher light levels. This variation appears to be part of a xanthophyll cycle that helps regulate
photosynthesis Photosynthesis ( ) is a system of biological processes by which photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical energy necessary to fuel their metabo ...
under different light conditions. Research published in 2018 showed that the fungal component of ''C. grayi'' contains
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s for producing protective compounds called pyrrolopyrazines (PPZ). Like many lichens, ''C. grayi'' produces various
secondary metabolite Secondary metabolites, also called ''specialised metabolites'', ''secondary products'', or ''natural products'', are organic compounds produced by any lifeform, e.g. bacteria, archaea, fungi, animals, or plants, which are not directly involved ...
s – chemicals that are not essential for basic life functions but help the organism survive. The PPZ compounds appear to help protect the lichen against insects that might try to eat it. The genes responsible for making these compounds are grouped together in what scientists call a "
gene cluster A gene cluster is a group of two or more genes found within an organism's DNA that encode similar peptide, polypeptides or proteins which collectively share a generalized function and are often located within a few thousand base pairs of each othe ...
". This discovery was significant because previously, these types of genes were only known from certain insect-pathogenic fungi like ''
Metarhizium ''Metarhizium'' is a genus (biology), genus of entomopathogenic fungus, entomopathogenic fungi in the family Clavicipitaceae. With the advent of genetic profiling, placing these fungi in proper taxa has now become possible. Most turn out to be ...
'' species. Finding these genes in ''C. grayi'' helped scientists understand that this
chemical defense Chemical defense is a strategy employed by many organisms to avoid consumption by producing toxic or repellent metabolites or chemical warnings which incite defensive behavioral changes. The production of defensive chemicals occurs in plants, fung ...
system is much older than previously thought, dating back to the early evolution of a major group of fungi called
Pezizomycotina Pezizomycotina is the largest subdivision of Ascomycota, containing the filamentous ascomycetes and most lichenized fungi. It is more or less synonymous with the older taxon Euascomycota. These fungi reproduce by fission rather than budding. Thi ...
.


Similar species

''Cladonia grayi'' is a member of the ''C. chlorophaea'' group, a complex of morphologically similar lichens that some researchers have historically considered to be merely chemical variants of the same species. However, ''C. grayi'' maintains several distinguishing characteristics that support its status as a distinct species, including its podetia with surfaces (rarely heavily sorediate) and its characteristically dark colour. While ''C. grayi'' can be confused with related species, its closest look-alike is '' C. merochlorophaea'', from which it can be distinguished by its smaller cups (scyphi) and less powdery surface texture. ''C. merochlorophaea'' typically displays more obvious powdery areas (soredia), especially in the central portions of its podetia. Another possible lookalike, '' C. rei'', tends to have narrower cups than ''C. grayi'', while '' C. pleurota'' can generally be differentiated by its overall yellow-green colour and reddish apothecia and pycnidia. However, due to the subtle nature of these morphological differences, definitive identification often requires
thin-layer chromatography Thin-layer chromatography (TLC) is a chromatography technique that separates components in non-volatile mixtures. It is performed on a TLC plate made up of a non-reactive solid coated with a thin layer of adsorbent material. This is called the sta ...
to analyze the specific lichen substances present. ''Cladonia grayi'' often produces abundant small, leaf-like squamules, which was historically recognised as the form ''squamulosa''. While this squamulose form can be confused with ''C. asahinae'', which also frequently develops squamules on its podetia, the two species can be readily distinguished by their different chemical compositions. When ''C. grayi'' lacks squamules entirely, it becomes very difficult to distinguish from ''C. merochlorophaea'' based on morphology alone, and chemical analysis becomes necessary for definitive identification.


Development

The development of a lichen symbiosis in ''Cladonia grayi'' involves five main stages: a pre-contact stage where chemical signalling occurs between the fungus and alga without physical contact, a contact stage where they first physically connect, an envelopment stage where fungal hyphae surround the algal cells, an incorporation stage forming an undifferentiated pre-thallus, and finally a differentiation stage producing the complex thallus structure. During these stages, both partners show coordinated changes in
gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
that facilitate their symbiotic relationship. Research has shown that ''C. grayi'' has a highly specific response when encountering its compatible photobiont ''Asterochloris''. While the fungus can grow over various surfaces and organisms, it only displays a distinctive growth pattern involving increased lateral branching when it contacts ''Asterochloris'' cells. This selective response is part of the early contact stage of lichen development, though not all algal cells trigger this response, suggesting that factors like cell age may influence successful symbiotic initiation. When grown with other green algae like ''
Chlorella vulgaris ''Chlorella vulgaris'' is a species of green microalga in the division Chlorophyta. This unicellular alga was discovered in 1890 by Martinus Beijerinck, Martinus Willem Beijerinck as the first microalga with a well-defined nucleus. It is the typ ...
'' or '' Trentepohlia'' species that are never found associated with ''C. grayi'' in nature, the fungus shows no specialised growth response, demonstrating the specificity of the fungus-alga recognition system. The development of ''Cladonia grayi'' follows a distinct pattern that can be traced through the growth of its fungal
meristem In cell biology, the meristem is a structure composed of specialized tissue found in plants, consisting of stem cells, known as meristematic cells, which are undifferentiated cells capable of continuous cellular division. These meristematic c ...
tissue. In early
ontogeny Ontogeny (also ontogenesis) is the origination and development of an organism (both physical and psychological, e.g., moral development), usually from the time of fertilization of the ovum, egg to adult. The term can also be used to refer to t ...
, when the
podetium A podetium (plural: podetia) is the upright secondary thallus in ''Cladonia'' lichens. It is a hollow stalk extending from the . Podetia can be pointed stalks, club like, cupped, or branched in shape and may or may not contain the ascocarp, the f ...
(the erect ) is about 100 Î¼m tall, it begins as an , vertically oriented mass of fungal tissue. The upper surface starts as a slightly concave disc composed primarily of meristematic tissue, with few loose
hypha A hypha (; ) is a long, branching, filamentous structure of a fungus, oomycete, or actinobacterium. In most fungi, hyphae are the main mode of vegetative growth, and are collectively called a mycelium. Structure A hypha consists of one o ...
e or algal cells near the apex. As development continues, the meristem tissue thins toward the centre of the disc while the margin expands both outward and vertically. The species exhibits two main developmental phases in its cup formation. In the first phase, while the contiguous meristem grows uniformly, the cup maintains a roughly symmetrical shape with a circular margin. During the second phase, the previously continuous meristematic tissue at the margin divides into separate bundles, which can develop into apothecia, pycnidia, or lichenised proliferations. Some podetia, particularly those growing in exposed conditions, may maintain wider, shallower cups with a continuous meristematic margin, while others, typically found in less exposed conditions, develop proliferations from the cup margin. A distinctive feature of ''C. grayi''s development is its subtly articulated spiral growth pattern, which becomes most apparent in branching proliferations growing along the cup margin. As the podetium matures, one portion of the meristematic tissue often grows faster than the rest, creating an asymmetrical cup with an oblique margin. This faster-growing section typically carries the largest bundle of meristematic tissue at its apex and may become the dominant proliferation. The proliferations can branch further, developing into various forms including narrowly branched, blunt, or swollen-laminar structures, with the meristematic tissue at their apices following a spiral growth pattern.


Photobiont

The of ''Cladonia grayi'' is '' Asterochloris glomerata'', a unicellular
green alga The green algae (: green alga) are a group of chlorophyll-containing autotrophic eukaryotes consisting of the phylum Prasinodermophyta and its unnamed sister group that contains the Chlorophyta and Charophyta/ Streptophyta. The land plants ( ...
belonging to the
Trebouxiales The Trebouxiales are an order (biology), order of green algae in the Class (biology), class Trebouxiophyceae. References

Trebouxiales, Chlorophyta orders {{green algae-stub ...
, which is the most common order of lichen algae. The ''A. glomerata''
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
is about 56
megabase A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
s (Mb) in size and contains around 10,000 gene models. This genome size is significantly smaller than that of ''
Chlamydomonas reinhardtii ''Chlamydomonas reinhardtii'' is a single-cell green alga about 10 micrometres in diameter that swims with two flagella. It has a cell wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid, and a ...
'' (120 Mb) but larger than those of other
Trebouxiophyceae The Trebouxiophyceae, also known as trebouxiophytes, are a class of green algae, in the division Chlorophyta. Members of this class are single-celled, colonial, or multicellular and are found in freshwater, terrestrial or marine habitats worldwid ...
like '' Coccomyxa subellipsoidea'' C-169 (49 Mb) and ''
Chlorella variabilis ''Chlorella'' is a genus of about thirteen species of single-Cell (biology), celled or Colony (biology), colonial green algae of the division Chlorophyta. The cells are spherical in shape, about 2 to 10 Micrometre, μm in diameter, and are with ...
'' NC64A (46.2 Mb). During the initial stages of symbiosis formation, ''A. glomerata'' and the fungal partner show coordinated changes in gene expression related to metabolic exchange. The photobiont upregulates genes encoding extracellular
hydrolase In biochemistry, hydrolases constitute a class of enzymes that commonly function as biochemical catalysts that use water to break a chemical bond: :\ce \quad \xrightarrowtext\quad \ce This typically results in dividing a larger molecule into s ...
s and
membrane transport In cellular biology, membrane transport refers to the collection of mechanisms that regulate the passage of solutes such as ions and small molecules through biological membranes, which are lipid bilayers that contain proteins embedded in them. Th ...
proteins, while matching increases occur in the expression of ammonium and ribitol transporters in the fungus. This synchronised genetic response facilitates the metabolic interactions necessary for successful lichenisation. Analysis of the ''A. glomerata'' genome revealed several distinctive features related to its role as a lichen photobiont. The alga possesses
meiosis Meiosis () is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, the sperm or egg cells. It involves two rounds of division that ultimately result in four cells, each with only one c ...
-specific genes, supporting the occurrence of
sexual reproduction Sexual reproduction is a type of reproduction that involves a complex life cycle in which a gamete ( haploid reproductive cells, such as a sperm or egg cell) with a single set of chromosomes combines with another gamete to produce a zygote tha ...
in its free-living stage, which has implications for lichen adaptability. The genome also shows evidence of
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the e ...
, including a large
viral DNA A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and t ...
insertion of approximately 540 kilobases, as well as genes likely acquired from
archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
and
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
. Among these are genes potentially involved in stress resistance, including archaeal
ATPase ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, ATP hydrolase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion or ...
s and bacterial
desiccation Desiccation is the state of extreme dryness, or the process of extreme drying. A desiccant is a hygroscopic (attracts and holds water) substance that induces or sustains such a state in its local vicinity in a moderately sealed container. The ...
-related proteins. Notable expansions in
gene families A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions. One such family are the genes for human hemoglobin subunits; the ten genes are in two clusters on ...
were observed in ''A. glomerata'', including
kinase In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule don ...
s,
carbohydrate A carbohydrate () is a biomolecule composed of carbon (C), hydrogen (H), and oxygen (O) atoms. The typical hydrogen-to-oxygen atomic ratio is 2:1, analogous to that of water, and is represented by the empirical formula (where ''m'' and ''n'' ...
-active enzymes, and
ankyrin Ankyrins are a family of proteins that mediate the attachment of integral membrane proteins to the spectrin-actin based membrane cytoskeleton. Ankyrins have binding sites for the beta subunit of spectrin and at least 12 families of integral mem ...
domain proteins. The alga also shows a reduced set of
nitrate Nitrate is a polyatomic ion with the chemical formula . salt (chemistry), Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are solubility, soluble in wa ...
assimilation genes compared to other green algal genomes, suggesting adaptation to obtaining nitrogen primarily from its fungal partner. Additionally, ''A. glomerata'' has retained proteins associated with flagellar motility, matching microscopic observations of flagellated
zoospore A zoospore is a motile asexual spore that uses a flagellum for locomotion in aqueous or moist environments. Also called a swarm spore, these spores are created by some protists, bacteria, and fungi to propagate themselves. Certain zoospores are ...
s and
gamete A gamete ( ) is a Ploidy#Haploid and monoploid, haploid cell that fuses with another haploid cell during fertilization in organisms that Sexual reproduction, reproduce sexually. Gametes are an organism's reproductive cells, also referred to as s ...
s in its free-living state, though these structures are not present in the lichenised form.


Habitat and distribution

''Cladonia grayi'' is a widespread lichen species that demonstrates considerable adaptability in its choice of growing surfaces. It can be found on multiple substrates, including rotting wood, organic soil layers (
humus In classical soil science, humus is the dark organic matter in soil that is formed by the decomposition of plant and animal matter. It is a kind of soil organic matter. It is rich in nutrients and retains moisture in the soil. Humus is the Lati ...
), and bare ground, showing a strong preference for highly acidic conditions. While the species has a nearly
cosmopolitan distribution In biogeography, a cosmopolitan distribution is the range of a taxon that extends across most or all of the surface of the Earth, in appropriate habitats; most cosmopolitan species are known to be highly adaptable to a range of climatic and en ...
, it is most abundant in the Northern Hemisphere, particularly in Arctic and
temperate In geography, the temperate climates of Earth occur in the middle latitudes (approximately 23.5° to 66.5° N/S of the Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ran ...
regions. In
Mediterranean The Mediterranean Sea ( ) is a sea connected to the Atlantic Ocean, surrounded by the Mediterranean basin and almost completely enclosed by land: on the east by the Levant in West Asia, on the north by Anatolia in West Asia and Southern ...
areas, it is relatively uncommon, occurring in scattered populations primarily in meso- to supramediterranean zones, and showing a preference for Eurosiberian regions from
colline ''Colline'' is a 1929 novel by the French writer Jean Giono. It has also been published as ''Hill of Destiny''. It tells the story of a small hamlet in Provence where the superstitious residents struggle against nature, as their settlement is str ...
to
montane Montane ecosystems are found on the slopes of mountains. The alpine climate in these regions strongly affects the ecosystem because temperatures lapse rate, fall as elevation increases, causing the ecosystem to stratify. This stratification is ...
elevations. The species is also present in the Southern Hemisphere, with documented occurrences in both
Neotropical The Neotropical realm is one of the eight biogeographic realms constituting Earth's land surface. Physically, it includes the tropical terrestrial ecoregions of the Americas and the entire South American temperate zone. Definition In biogeogra ...
regions and
Australasia Australasia is a subregion of Oceania, comprising Australia, New Zealand (overlapping with Polynesia), and sometimes including New Guinea and surrounding islands (overlapping with Melanesia). The term is used in a number of different context ...
, though these populations tend to be more dispersed and are typically found at higher altitudes. ''Cladonia grayi'' appears to be the most common member of the ''C. chlorophaea'' group in Belarus, where it represents approximately 40% of specimens examined in a comprehensive survey. Two
chemotype A chemotype (sometimes chemovar) is a chemically distinct entity in a plant or microorganism, with differences in the composition of the secondary metabolites. Minor genetic and epigenetic changes with little or no effect on morphology or anatomy ...
s have been documented in Belarus with roughly equal frequency: one containing only grayanic acid and 4-''O''-demethylgrayanic acid, and another that additionally contains substances of the
fumarprotocetraric acid Fumarprotocetraric acid is a chemical compound with the chemical formula . It is a secondary metabolite produced by a variety of lichens. Occurrence Fumarprotocetraric acid is mainly known for its occurrence in Iceland moss (''Cetraria islandica ...
complex. The species shows distinct ecological preferences in Belarus, being found primarily (90%) in
pine A pine is any conifer tree or shrub in the genus ''Pinus'' () of the family Pinaceae. ''Pinus'' is the sole genus in the subfamily Pinoideae. ''World Flora Online'' accepts 134 species-rank taxa (119 species and 15 nothospecies) of pines as cu ...
forests across a range of humidity conditions, from wet boggy areas to extremely dry stands. It has been documented growing on various substrates including pine bark, soil, decaying wood,
juniper Junipers are coniferous trees and shrubs in the genus ''Juniperus'' ( ) of the cypress family Cupressaceae. Depending on the taxonomy, between 50 and 67 species of junipers are widely distributed throughout the Northern Hemisphere as far south ...
,
oak An oak is a hardwood tree or shrub in the genus ''Quercus'' of the beech family. They have spirally arranged leaves, often with lobed edges, and a nut called an acorn, borne within a cup. The genus is widely distributed in the Northern Hemisp ...
,
birch A birch is a thin-leaved deciduous hardwood tree of the genus ''Betula'' (), in the family Betulaceae, which also includes alders, hazels, and hornbeams. It is closely related to the beech- oak family Fagaceae. The genus ''Betula'' contains 3 ...
,
hornbeam Hornbeams are hardwood trees in the plant genus ''Carpinus'' in the family Betulaceae. Its species occur across much of the temperateness, temperate regions of the Northern Hemisphere. Common names The common English name ''hornbeam'' derives ...
and
alder Alders are trees of the genus ''Alnus'' in the birch family Betulaceae. The genus includes about 35 species of monoecious trees and shrubs, a few reaching a large size, distributed throughout the north temperate zone with a few species ex ...
bark, though chemotype I tends to occur more frequently on acidic tree bark while chemotype II is more commonly found on soil and wood.


See also

* List of ''Cladonia'' species


References

{{Taxonbar , from1=Q3678889 , from2=Q108583193 , from3=Q108546632 grayi Lichen species Lichens described in 1929 Lichens of Asia Lichens of Australasia Lichens of Europe Lichens of North America Lichens of South America Lichens of Southern Africa Taxa named by Heinrich Sandstede