Genomic and Fossil Windows Into the Secret Lives of the Most Ancient Fungi
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REVIEWS Genomic and fossil windows into the secret lives of the most ancient fungi Mary L. Berbee 1 ✉ , Christine Strullu- Derrien 2,3, Pierre- Marc Delaux 4, Paul K. Strother5, Paul Kenrick 2, Marc- André Selosse 3,6 and John W. Taylor 7 Abstract | Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi. Fungi are crucial for thriving land plant communities as enzymes surely kept pace3,16,17. Comparative analy- mycorrhizal symbionts1,2 and decomposers3. For perhaps sis of genomes of land plants18 and their closest algal 500 million years4,5, fungi have been supplying land plants relatives19,20 reveals the evolutionary origins of constitu- with phosphorus and other minerals, thereby speeding ents of plant immune systems that are fundamental both up photosynthesis and contributing to the drawdown for defence against fungal parasites and for the evolution 6–8 mycorrhizae21 1Department of Botany, of atmospheric carbon dioxide . Yet phylogenom- of . Green algae and, by extension, the fungi University of British Columbia, ics tells us that fungi originated far earlier, deep in the that they nourished may have begun to evolve in fresh- Vancouver, BC, Canada. Precambrian9, perhaps a billion years ago2,10. This infor- water environments, likely in the Precambrian, a billion 2Department of Earth mation raises two important questions: when did fungi years ago, as highlighted by the geology22,23 and recent Sciences, The Natural History emerge, and what were their early lifestyles? analysis of the phylogenies of algae24,25. Museum, London, UK. How and when fungi diversified and adapted to their We address the puzzle of what could have nourished 3Institut Systématique present roles in Earth systems have long been hidden. early fungi prior to the origin of land plants by review- Evolution Biodiversité, Muséum national d’Histoire Fossils representing simple filaments or spores of ancient ing geological evidence of other life forms in shallow 22,23,26 naturelle, CNRS, Sorbonne fungi are uncommon in the Precambrian fossil record, marine and terrestrial environments . We go on Université, Paris, France. and difficult to recognize or to distinguish from other to consider specific fossils and compare their dates 11 4LRSV, Université de Toulouse, organisms . Due largely to a lack of reliable fossil cali- and traits with fungal phylogenies based on genomic CNRS, UPS, Castanet-Tolosan, brations, comparisons of ages depend on dated fungal analy ses, asking which sorts of geological and fossil France. and plant phylogenies2,12, providing a stimulating frame- data can be used to resolve conflicts between rocks and 5Department of Earth and work for thought, but these estimates are too impre- clocks. Recently, Loron et al.27 published evidence of Environmental Sciences, cise to eliminate alternative hypotheses about ancient 1 billion-year-old fungal fossils from Arctic Canada that Boston College, Weston, MA, USA. ecological relationships between kingdoms. they named Ourasphaira giraldae. A 1 billion- year- old 6Department of Plant Here, we review recent landmark studies that open fungus is twice the age of land plants, based on either 2,4 Taxonomy and Nature new windows on the understanding of the earliest fungi. fossils or molecular dating . This and other surpris- Conservation, University Comparative analysis of genomes provides the most ing fossil results invite challenge. We review the evidence of Gdańsk, Gdańsk, Poland. direct available evidence of ancient interdependence for interpreting Precambrian fossils as ‘fungi’28,29, dis- 7Department of Plant and between fungi and algae or land plants. Fungi survive cuss the early occurrences of Palaeozoic fungi and high- Microbial Biology, University by secreting digestive enzymes and taking up the freed light the potential contributions of new tools towards of California, Berkeley, 13,14 CA, USA. nutrients . The record — at least the remaining record resolving their identities, for example, confocal scanning 30 27,29,31 ✉e- mail: mary.berbee@ — of the origin of enzymes targeting algal or plant cell laser microscopy , synchrotron analyses and chem- 27,29 botany.ubc.ca walls is embedded in fungal genomes. As green algae ical analyses . We document the tremendous strides https://doi.org/10.1038/ evolved into land plants, and as the polysaccharides that have been made in characterizing fossils microscop- s41579-020-0426-8 in their cell walls diversified15, the evolution of fungal ically and chemically, but worry that even greater ones NATURE REVIEWS | MICROBIOLOGY REVIEWS will be needed when the specimens are hundreds of mil- The first fungi: nutrition and ecology lions to billions of years old and have endured pressures Modern fungi evolved from phagotrophic, aerobic ances- and temperatures far beyond those experienced by living tors. Within the eukaryotic tree of life, fungi together organisms. with the nucleariid amoebas are the closest relatives of Holozoa32. Over a billion years ago2,10, the fungal line- Precambrian Phanerozoic age evolved as a grade of motile, unicellular, amoeboid protists (Fig. 1). The first amoeboid fungi may have been h 33 (Fig. 1) Dikarya Basidiomycota free living and, much like modern nucleariids 34 Osmotrophs Ascomycota and aphelids , equipped with filose pseudopodia and a g Fungi Mucoromycota, phagotrophic mode of nutrition that involved engulfing f Glomeromycotina 35,36 Terrestrial fungi and digesting organisms smaller than themselves . g Mucoromycota, Phagotrophs diversified, giving rise to obligate parasites Mucoromycotina such as Rozella, which engulf and digest the cytoplasm Zoopagomycota e within a single host cell37,38, and microsporidia, which Chytridiomycota Blastocladiomycota lost the capacity for phagotrophy while refining their adaptations as intracellular parasites39. In contrast to Fungi and Rozella the ancestral phagotrophs, the vast majority of modern allied protists c Microsporidia fungi, from aquatic or semi- aquatic Chytridiomycota Phagotrophs Aphelids to the land- inhabiting yeasts, moulds and mushrooms Opisthokonts Nucleariids of Dikarya, are osmotrophic13,14 (Fig. 1). This mode of Sphaeroforma feeding involves the cytoplasmic uptake of nutrients Collar flagellates that diffuse across cell walls and often is coupled with Holozoa, animals and allied protists Insects the secretion by the fungus of extracellular enzymes that Vertebrates release nutrients from substrates. Comb jellies Fungi are almost all obligate aerobes or facultative Slime moulds anaerobes that require oxygen to complete their life g cycles. Oxygen is needed for oxidative phosphoryl- Land plants Vascular plants ation and for sterol biosynthesis. Additionally, genomes e Bryophytes of early diverging fungi, including Rozella allomycis, Streptophytes Charophyceae d Chytridiomycota16, Zoopagomycota and Dikarya10, Mesostigma b encode lytic polysaccharide monooxygenases, enzymes Chlorophyte that require oxygen to facilitate breakdown of poly- Red algae saccharides40. Just two groups of obligate anaerobic 4 fungi are known and both independently lost the ances- tral aerobic lifestyle. Microsporidia are one group; they Fungal origins in freshwater and 5 diversification with streptophyte algae live inside animal cells and compensate for the loss of their mitochondria and absence of oxidative respir- 3 1 2 h ation by absorbing nutrients and even ATP from their 41 b e g surrounding hosts . The other group, the rumen a fungi (Neocallimastigomycotina in Chytridiomycota), c adapted to the anaerobic, cellulose- rich environment d f in the digestive systems of herbivores. This adaptation has involved gain from rumen bacteria, by horizontal transfer, of multiple genes in several pathways needed for anaerobiosis42. Given the rarity of obligately anaerobic 1,600 1,200 800 400 0 Millions of years ago fungi, it seems safe to state that the primary evolution- Fig. 1 | Evolution of early fungi. Fungi and animals evolved in the Precambrian from ary radiation of their kingdom occurred in oxygenated phagotrophic, amoeba-like ancestors that engulf nutrients into food vacuoles within environments. their cells and left no known fossil record. The dated phylogeny (top) shows that modern, multicellular fungi descended from unicellular phagotrophs that evolved cell walls and Plants are key to evolutionary success of osmotrophic became osmotrophic, secreting digestive enzymes into the surrounding environment. Fungi fungi. Modern land plants provide fungi with a superb originated in freshwater and undertook several evolutionary transitions (bottom). Stage 1: source of reliable energy. Much of the carbon from net Predating fungi, fossils of cyanobacteria are known from freshwater89 and marine habitats