Rock-inhabiting fungi: terminology, diversity, evolution and adaptation mechanisms

Figures & data

Table 1. Characteristics comparison between typical and nontypical rock fungi

Characteristics	lithophilic (typical) RIF		lithotolerant (nontypical) RIF
	Niche	Culture	Niche	Culture
Habitats	rocks		rocks and other niches
Growth	extremely slow	extremely slow	slow	moderate
Melanized cell wall	+	+	+	+
Microcolonial appearance	+	+	-	-
Thicken cell wall	+	+	±	±
Meristematic development	+	+	-	-
Black yeast form	±	±	±	±
Sporulation	-	-	-	±

Figure 1. Growth rate comparison on culture plates between litholithic fungi and lithotolerant fungi of rock-inhabiting fungi. Values of plots represents growth rates (mm. per week) of published RIF species on culture plates. Significant difference between green and Orange plots represents the distinction between typical and nontypical RIF.

Table 2. Species numbers and their affiliation of rock-inhabiting fungi

Phylum	Class	Subclass	Order	Family	Genus	Total RIF species	New species	Typical RIF	Nontypical RIF
Ascomycota	-	-	-	-	Knufia	9	9	9	0
	Dothideomycetes	-	-	-	Cryomyces	4	, 4	4	0
		-	-	-	Rupestriomyces	3	3	3	0
		-	-	-	Saxomyces	2	2	2	0
		-	-	-	Spissiomyces	3	2	3	0
		-	Coniosporiales	Coniosporiaceae	Coniosporium	3	3	3	0
		Dothideomycetidae	Capnodiales	-	Arthrocatena	1	1	1	0
				-	Capnobotryella	5	4	5	0
				-	Catenulomyces	1	1	1	0
				-	Constantinomyces	6	6	6	0
				-	Elasticomyces	1	1	1	0
				-	Friedmanniomyces	2	2	2	0
				-	Hyphoconis	1	1	1	0
				-	Incertomyces	2	2	2	0
				-	Lapidomyces	1	1	1	0
				-	Meristemomyces	1	1	1	0
				-	Monticola	1	1	1	0
				-	Oleoguttula	1	1	1	0
				-	Penidiella	1	0	1	0
				-	Perusta	1	1	1	0
				-	Pseudotaeniolina	1	1	1	0
				-	Ramimonilia	1	1	1	0
				-	Recurvomyces	1	0	1	0
				-	Saxophila	1	1	1	0
				-	Vermiconidia	4	4	4	0
				Aeminiaceae	Aeminium	1	1	1	0
				Capnodiaceae	Leptoxyphium	>1	0	0	1
				Paradevriesiaceae	Paradevriesia	1	1	1	0
				Teratosphaeriaceae	Acrodontium	>1	1	0	>1
					Austroafricana	>1	0	0	>1
					Catenulostroma	1	0	1	0
					Hortaea	2	0	2	0
					Neocatenulostroma	1	0	1	0
			Cladosporiales	Cladosporiaceae	Cladosporium	>10	0	0	>10
					Rachicladosporium	6	6	6	0
					Verrucocladosporium	>1	0	0	>1
			Dothideales	Dothioraceae	Aureobasidium	>1	0	0	>1
					Endoconidioma	>1	0	0	>1
					Hormonema	1	1	1	0
					Pringsheimia	>1	0	0	>1
			Mycosphaerellales	Extremaceae	Extremus	2	2	2	0
				Mycosphaerellaceae	Pseudocercospora	>1	0	0	>1
				Neodevriesiaceae	Neodevriesia	6	4	6	0
			Neophaeothecales	Neophaeothecaceae	Neophaeotheca	1	0	1	0
			Phaeothecales	Phaeothecaceae	Phaeotheca	>1	0	0	>1
		Pleosporomycetidae	Pleosporales	-	Phoma	>5	0	0	>5
				Periconiaceae	Periconia	>5	0	0	>5
				Pleosporaceae	Alternaria	>5	0	0	>5
			Venturiales	Sympoventuriaceae	Ochroconis	2	2	0	2
	Eurotiomycetes	Eurotiomycetidae	-	-	Sarcinomyces	1	1	1	0
			Chaetothyriales	-	Bacillicladium	1	1	1	0
				-	Bradymyces	4	4	4	0
				-	Neophaeococcomyces	>1	0	0	>1
				Cyphellophoraceae	Cyphellophora	2	2	2	0
				Herpotrichiellaceae	Cladophialophora	5	4	5	0
					Exophiala	6	5	6	0
					Phaeococcomyces	1	0	1	0
					Phialophora	1	0	1	0
					Rhinocladiella	1	0	1	0
				Trichomeriaceae	Anthracina	1	1	1	0
					Lithohypha	2	2	2	0
					Trichomerium	4	4	4	0
			Eurotiales	Aspergillaceae	Aspergillus	>10	0	0	>10
					Penicillium	>10	0	0	>10
1	2	3	11	19	64	>175	95	108	>65

*Family and genus names in bold are novel taxa of rock-inhabiting fungi

Figure 2. Distribution of rock-inhabiting fungi. Size of blue circles represents the genus number of rock-inhabiting fungi.

Table 3. Genomes of rock-inhabiting fungi and related strains

Species	Strain	Genome size (Mb)	GC (%)	Repeat (%)	tRNA	Gene	Location/Substrate	Reference
Coniosporium apollinis	CBS 100218	28.51	52.13	28	-	11,886	Microcolonial fungi, mediterranean region	Sterflinger et al. 2014
Cryomyces antarcticus	MA 5682	24.32	53.84	33	-	10,731	Cryptoendolithic fungi, Antarctica	Sterflinger et al. 2014
Friedmanniomyces endolithicus	CCFEE 5311	46.75	56.5	-	43	18,070	Cryptoendolithic fungi, Antarctica	Coleine et al. 2020
Friedmanniomyces simplex	CCFEE 5184	37.79	56.6	-	22	13,788	Cryptoendolithic fungi, Antarctica	Coleine et al. 2020
Hortaea thailandica	CCFEE 6315	23.89	55.5	-	23	8,801	Cryptoendolithic fungi, Antarctica	Coleine et al. 2020
Rachicladosporium antarcticum	CCFEE 5527	47.4	-	-	-	18,781	Cryptoendolithic fungi, Antarctica	Coleine et al. 2017
Rachicladosporium sp.	CCFEE 5018	-	-	-	-	18,892	Cryptoendolithic fungi, Antarctica	Coleine et al. 2017
Acidomyces acidophilus	BFW	21.87	54.8	-	41	10,549	Richmond Mine, California	Coleine et al. 2020
Baudoinia panamericana	UAMH 10762	29.88	49.5	-	-	-	Ethanol vapor	Coleine et al. 2020
Cladosporium sphaerospermum	UM 843	26.13	55.87	29	-	16,622	ubiquitous hyphomycte	Sterflinger et al. 2014
Exophiala dermatitidis	NIH/UT8656	26.37	51.51	33	-	10,020	opportunistics	Sterflinger et al. 2014
Hortaea werneckii	EXF-2000	49.89	53.5	-	28	15,649	Marine solar salterns, Slovenia	Coleine et al. 2020
Hortaea werneckii	EXF-2000	51.62	53.58	27	-	26,313	hypersaline	Sterflinger et al. 2014

*Species name in bold are typical rock-inhabiting fungi

Sterflinger K, Lopandic K, Pandey RV, Blasi B, Kriegner A. 2014. Nothing special in the specialist? Draft genome sequence of Cryomyces antarcticus, the most extremophilic fungus from Antarctica. PLoS One. 9(10):e109908. doi:https://doi.org/10.1371/journal.pone.0109908.

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Coleine C, Masonjones S, Sterflinger K, Onofri S, Selbmann L, Stajich JE. 2020. Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus. Fungal Biol. 124(5):458–467. doi:https://doi.org/10.1016/j.funbio.2020.01.005.

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Coleine C, Masonjones S, Selbmann L, Zucconi L, Onofri S, Pacelli C, Stajich JE. 2017. Draft genome sequences of the Antarctic endolithic fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018. Genome Announc. 5(27):e00397–00317. doi:https://doi.org/10.1128/genomeA.00397-17.

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