History
Soil fungi
Fungi have an enormous diversity on earth (Hyde et al. 2020, Liimatainen et al. 2020). Belowground fungal communities have a high diversity compared to other terrestrial ecosystems (Bridge & Spooner 2001, Tedersoo et al. 2022). They are most prominent in soil-biota, accounting for around 90% of the total microbial biomass (Bills et al. 2004). Various edaphic factors can boost or suppress the fungal community assemblage throughout the globe (Fracetto et al. 2013, Frac et al. 2018). Fungi contribute in ecosystem functioning by mediating nutrient cycling of carbon, nitrogen and phosphorous, plant growth and development, and in dead material decomposition (van der Heijden et al. 2008). They can be present as saprobes, mutualistic organisms (mycorrhizal) and/or pathogens in soil.
In the past, taxonomy and detection of soil fungi were based on morphology. Direct inoculation (Waksman 1916), dilution plates method (Warcup 1950), immersion tubes (Chesters 1948), and baiting method (Butler 1907) were commonly used for colony isolation and recovery of Alternaria, Fusarium, Mortierella, Penicillium, Trichoderma, etc., in different studies (Warcup 1950, Chesters & Thornton 1956). During 1980s molecular methods were introduced; i.e. denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), amplified rDNA restriction analysis (ARDRA), cloning and genetic fingerprinting techniques, which helped to picture the unculturable taxa those dwell in soil (Sudhakar et al. 2018, Wu et al. 2019). In recent times, HTS (High throughput sequencing) technologies were developed empowering the taxonomy community and diversity studies of fungi. Currently, ‘Next-generation sequencing’ (NGS) and ‘Third generation sequencing’ (TGS), are the most popular in global soil studies (Wu et al. 2019, Tedersoo et al. 2021). This paved the way to recover cryptic taxa, groups in large land areas, studying the family and/or class level, in spite that cultures are important in species identification. Thus, both HTS and culture based morpho-molecular methods are being used for various soil studies (Wu et al. 2019, Chethana et al. 2020).
Aspergillus, Fusarium, Penicillium and Trichoderma are common genera in soil, recovered from many parts of the world by the use of both culturing and HTS methods (Tedersoo et al. 2017, Wang & Zhuang 2022). Recent studies have isolated strains of genera which used to be rare in the soil; i.e. Calvatia, Chloridium, Cortinarius, Exophiala, Juxtiphoma, Kionochaeta, Kosmimatamyces, Ogataea, Phialoparvum, Pichia, Plectosphaerella, and Zygoascus (Groenewald et al. 2018, Giraldo, et al. 2019, Yasanthika et al. 2022).
Species identification in soil is critical and some of the cultures are sources of biotechnology as HTS methods are still lagged behind (Gutleben et al. 2018, Hyde et al. 2019). Thus, we use culturing and morpho-molecular approaches in their identification. In https://soilfun.org/ present genera and species introduced or recorded from soils all over the world.
References
Bills GF, Christensen MA RTHA, Powell MARTHA, Thorn GREG. 2004 – Saprobic soil fungi. Biodiversity of fungi: Inventory and monitoring methods 271–302.
Chesters CGC. 1948 – A contribution to the study of fungi in the soil. Transactions of the British Mycological Society. 30, 100–113
Butler EJ. 1907 – An account of the genus Pythium and some Chytridiaceae. Mem. Dep. Agric. India, Bot. Ser., 1(5), 1–162.
Chethana KWT, Jayawardena RS, Hyde KD. 2020 – Hurdles in fungal taxonomy: Effectiveness of recent methods in discriminating taxa. Megataxa 1(2), 114–122.
Crous PW, Wingfield M.J, Chooi YH, Gilchrist C L et al. 2020– Fungal Planet description sheets: 1042–1111. Persoonia: Molecular Phylogeny and Evolution of Fungi, 44, 301.
Frąc M, Hannula SE, Bełka M, Jędryczka M. 2018 – Fungal biodiversity and their role in soil health. Frontiers in Microbiology 9, 707.
Fracetto GGM, Azevedo LCB, Fracetto FJC, Andreote FD et al. 2013 – Impact of Amazon land use on the community of soil fungi. Scientia Agricola 70(2), 59–67.
Giraldo A, Hernández-Restrepo M, Crous PW. 2019 – New plectosphaerellaceous species from Dutch garden soil. Mycological Progress, 18(9), 1135-1154
Groenewald M, Lombard L, de Vries M, Lopez AG et a. 2018 – Diversity of yeast species from Dutch garden soil and the description of six novel Ascomycetes. FEMS Yeast Research, 18(7), foy076.
Gutleben J, Chaib De Mares M, Van Elsas, JD, Smidt H et al. 2018 – The multi-omics promise in context: from sequence to microbial isolate. Critical reviews in microbiology, 44, 212–229.
Hyde KD, Xu JC, Rapior S, Jeewon R et al. 2019 – The amazing potential of fungi: 50 ways we can exploit fungi industrially. Fungal Diversity 97: 1–136
Liimatainen K, Niskanen T, Dima B, Ammirati JF et al. 2020 – Mission impossible completed: unlocking the nomenclature of the largest and most complicated subgenus of Cortinarius, Telamonia. Fungal Diversity, 104(1), 291–331.
Rao S, Hyde KD, Pointing SB. 2013 – Comparison of DNA and RNA, and cultivation approaches for the recovery of terrestrial and aquatic fungi from environmental samples. Current microbiology 66, 185–191.
https://doi.org/10.1007/s00284-012-0256-7
Sathya A, Vijayabharathi R, Gopalakrishnan S. 2016 – Soil microbes: the invisible managers of soil fertility. In Microbial inoculants in sustainable agricultural productivity (pp. 1–16). Springer, New Delhi.
Schmidt PA, Bálint M, Greshake B, Bandow C, Römbke J, Schmitt I. 2013 – Illumina metabarcoding of a soil fungal community. Soil Biology and Biochemistry 65, 128-132.
Tedersoo L, Bahram M, Puusepp R, Nilsson RH, James TY. 2017 – Novel soil-inhabiting clades fill gaps in the fungal tree of life. Microbiome 5, 42.
Tedersoo L, Mikryukov V, Anslan S, Bahram M et al. 2021 – The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Diversity 111, 573–588
Van Der Heijden MG, Bardgett RD, Van Straalen NM. 2008 – The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology letters 11(3), 296–310
Wang XC, Zhuang WY. (2022). New Species of Aspergillus (Aspergillaceae) from Tropical Islands of China. Journal of Fungi, 8(3), 225.
Warcup JH. 1950 – The soil-plate method for isolation of fungi from soil. Nature 166(4211), 117.
Wu B, Hussain M, Zhang W, Stadler M et al. 2019 – Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi. Mycology 10(3), 127–140.
Yasanthika E, Tennakoon DS, Farias ARG, Bhat DJ et al. 2022 – New soil-inhabiting Chaetosphaeriaceous records from Thailand. Asian Journal of Mycology 5(1), 16–30
Recent Genus
NeurosporaParacremonium
Amphichorda
Recent Species
Neurospora tetrasporaParacremonium apiculatum
Amphichorda cavernicola