Darksidea phi, sp. nov., a dark septate root-associated fungus in foundation grasses in North American Great Plains

LITERATURE CITED

• Albright MB, Johansen R, Lopez D, Steven B, Kuske CR, Dunbar J. 2018. Short-term transcriptional response of microbial communities to nitrogen fertilization in a pine forest soil. Appl Environ Microbiol. 84:00598–18.
   Web of Science ®Google Scholar
• Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data [cited April 2020]. http://www.bioinformatics.babraham.ac.uk/projects/fastqc
   Google Scholar
• Bankevich A, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19:455–77.
   PubMed Web of Science ®Google Scholar
• Barton K. 2019. Mu-Min: multi-Model Inference. R-package version 1.43.15.
   Google Scholar
• Bates D, Maechler M, Bolker B, Walker S. 2015. Fitting linear mixed-effects models using lme4. J Stat Softw. 67:1–48.
   Web of Science ®Google Scholar
• Berthelot C, Zegeye A, Gaber DA, Chalot M, Franken P, Kovács GM, Leyval C, Blaudez D. 2020. Unravelling the role of melanin in Cd and Zn tolerance and accumulation of three dark septate endophytic species. Microorganisms. 8:537.
   Web of Science ®Google Scholar
• Bokati D, Herrera J, Poudel R. 2016. Soil influences colonization of root-associated fungal endophyte communities of maize, wheat, and their progenitors. J Mycol. 2016:8062073.
   Google Scholar
• Borchsenius F. 2009. FastGap 1.2. Software distributed by the authors. [accessed 2020 May 18]. http://www.aubot.dk/FastGap_home.htm
   Google Scholar
• Bushnell B, Rood J, Singer E. 2017. BBMerge–accurate paired shotgun read merging via overlap. PloS ONE. 12:e0185056.
   PubMed Web of Science ®Google Scholar
• Carbone I, Kohn LM. 1999. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia. 91:553–56.
   Web of Science ®Google Scholar
• Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, and Tiedje JM. 2014. Ribosomal Database Project: Data and Tools for High Throughput rRNA Analysis. Nucleic Acids Research. 41:1–10.
   Google Scholar
• Dayarathne MC, Wanasinghe DN, Jones EBG, Chomnunti P, Hyde KD. 2018. A novel marine genus, Halobyssothecium (Lentitheciaceae) and epitypification of Halobyssothecium obiones comb. nov. Mycol Prog. 17:1161–71.
   Web of Science ®Google Scholar
• Gaber DA, Berthelot C, Camehl I, Kovács GM, Blaudez D, Franken P. 2020. Salt stress tolerance of dark septate endophytes is independent of melanin accumulation. Front Microbiol. 11:3158.
   Web of Science ®Google Scholar
• Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts. Mol Ecol. 2:113–18.
   PubMed Web of Science ®Google Scholar
• Glass NL, Donaldson G. 1995. Development of primer sets designed for use with PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol. 61:1323–30.
   PubMed Web of Science ®Google Scholar
• Groenewald JZ, Nakashima C, Nishikawa J, Shin HD, Park JH, Jama AN, Groenewald M, Braun U, Crous PW. 2013. Species concepts in Cercospora: spotting the weeds among the roses. Stud Mycol. 75:115–70.
   PubMed Web of Science ®Google Scholar
• Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 29:1072–75.
   PubMed Web of Science ®Google Scholar
• Haridas S, et al. 2020. 101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens. Stud Mycol. 96:141–53.
   PubMed Web of Science ®Google Scholar
• Haselwandter K, Read DJ. 1982. The significance of a root-fungus association in two Carex species of high-alpine plant communities. Oecologia. 53:352–54.
   PubMed Web of Science ®Google Scholar
• Herrera J, Khidir H, Eudy D, Porras-Alfaro A, Natvig D, Sinsabaugh R. 2010. Shifting fungal endophyte communities colonize Bouteloua gracilis: effect of host tissue and geographical distribution. Mycologia. 102:1012–26.
   PubMed Web of Science ®Google Scholar
• Ihrmark K, et al. 2012. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol. 82:666–77.
   PubMed Web of Science ®Google Scholar
• Jumpponen A, Herrera J, Porras-Alfaro Rudgers J. 2017. Biogeography of root-associated fungal endophytes. In: Tedersoo L, editor. Biogeography of Mycorrhizal Symbiosis. Tartu (Estonia): Springer Nature; p. 195–222.
   Google Scholar
• Jumpponen A, Trappe JM. 1998. Dark septate endophytes: a review of facultative biotrophic root-colonizing fungi. New Phytol. 140:295–310.
   PubMed Web of Science ®Google Scholar
• Kahle D, Wickham H. 2013. ggmap: spatial Visualization with ggplot2. R J. 5:144–61.
   Google Scholar
• Katoh K, Rozewicki J, Yamada KD. 2017. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20:1160–66.
   Web of Science ®Google Scholar
• Khidir H, Eudy D, Porras-Alfaro A, Herrera J, Natvig D, Sinsabaugh R. 2010. A general suite of fungal endophytes dominate the roots of two dominant grasses in a semiarid grassland. J Arid Environ. 74:35–42.
   Web of Science ®Google Scholar
• Knapp DG, et al. 2018. Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. Sci Rep. 8:6321.
   PubMed Web of Science ®Google Scholar
• Knapp DG, Imrefi I, Boldpurev E, Csíkos S, Berek-Nagy PJ, Akhmetova G, Otgonsuren B, Kovács GM. 2019. Root colonizing endophytic fungi of the dominant grass Stipa kryloyii from a Mogolian steppe grassland. Front Microbiol. 10:2565.
   Web of Science ®Google Scholar
• Knapp DG, Kovács GM, Zajta E, Groenewald JZ, Crous PW. 2015. Dark septate endophytic pleosporalean genera from semiarid areas. Persoonia. 35:87–100.
   PubMed Web of Science ®Google Scholar
• Knapp DG, Pintye A, Kovács GM. 2012. The dark side is not fastidious - dark septate endophytic fungi of native and invasive plants of semiarid sandy areas. PLoS ONE. 7:e32570.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 33:1870–74.
   PubMed Web of Science ®Google Scholar
• Lady Bird Johnson Wildflower Center. 2009. Bouteloua eriopoda. Austin: The University of Texas at Austin; [ accessed 2019 Oct 22]. https://www.wildflower.org/plants/result.php?id_plant=BOER4
   Google Scholar
• Lady Bird Johnson Wildflower Center. 2012. Bouteloua gracilis. Austin: The University of Texas at Austin; [ accessed 2019 Oct 22]. https://www.wildflower.org/plants/result.php?id_plant=bogr2
   Google Scholar
• Lady Bird Johnson Wildflower Center. 2015. Andropogon gerardii. Austin: The University of Texas at Austin; [ accessed 2019 Oct 22]. https://www.wildflower.org/plants/result.php?id_plant=ANGE
   Google Scholar
• Lady Bird Johnson Wildflower Center. 2018. Bouteloua dactyloides. Austin: The University of Texas at Austin; [ accessed 2019 Oct 22]. https://www.wildflower.org/plants/result.php?id_plant=BODA2
   Google Scholar
• Lady Bird Johnson Wildflower Center. 2019. Schizachyrium scoparium. Austin: The University of Texas at Austin; [ accessed 2019 Oct 22]. https://www.wildflower.org/plants/result.php?id_plant=SCSC
   Google Scholar
• Lagueux D, Jumpponen A, Porras-Alfaro A, Herrera J, Chung YA, Baur LE, Smith MD, Knapp AK, Collins SL, Rudgers JA. 2020. Experimental drought re-ordered assemblages of root-associated fungi across North American grasslands. Br Ecol Soc. 103:776–92.
   Google Scholar
• Li X, He X, Hou L, Ren Y, Wang S, Su F. 2018. Dark septate endophytes isolated from a xerophyte plant promote the growth of Ammopiptanthus mongolicus under drought conditions. Sci Rep. 8:7896.
   PubMed Web of Science ®Google Scholar
• Mandyam K, Jumpponen A. 2005. Seeking the elusive function of the root-colonising dark septate endophytic fungi. Stud Mycol. 53:173–89.
   Google Scholar
• Mandyam K, Loughin T, Jumpponen A. 2010. Isolation and morphological and metabolic characterization of common endophytes in annually burned tallgrass prairie. Mycologia. 102:813–21.
   PubMed Web of Science ®Google Scholar
• Nagy LG, Kocsubé S, Csana Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T. 2012. Re-mind the gap! Insertion– deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS ONE. 7:e49794.
   PubMed Web of Science ®Google Scholar
• Pereira E, Vázquez de Aldana BR, San Emeterio L, Zabalgogeazcoa I. 2019. A survey of culturable fungal endophytes from Festuca rubra subsp. pruinosa, a grass from marine cliffs, reveals a core microbiome. Front Microbiol. 9:3321.
   Web of Science ®Google Scholar
• Pintye A, Knapp DG. 2021. Two pleosporalean root-colonizing fungi, Fuscosphaeria hungarica gen. et sp. nov. and Delitschia chaetomioides, from a semiarid grassland in Hungary. Mycol Prog. 20:39–50.
   Web of Science ®Google Scholar
• Porras-Alfaro A, Bayman P. 2011. Hidden fungi, emergent properties: endophytes and microbiomes. Annu Rev Phytopathol. 49:291–315.
   PubMed Web of Science ®Google Scholar
• Porras-Alfaro A, Herrera J, Natvig D, Lipinski K, Sinsabaugh R. 2011. Diversity and distribution of soil fungal communities in a semiarid grassland. Mycologia. 103:10–21.
   PubMed Web of Science ®Google Scholar
• Porras-Alfaro A, Herrera J, Sinsabaugh R, Odenbach K, Lowrey T, Natvig D. 2008. Novel root fungal consortium associated with a dominant desert grass. Appl Environ Microbiol. 74:2805–13.
   PubMed Web of Science ®Google Scholar
• Porras-Alfaro A, Muniania-Nninga C, Hamm PS, Torres-Cruz TJ, Kuske CL. 2017. Fungal Diversity and Function in Desert Ecosystems. In: Steven B, editor. The Biology of Arid Soils Biology. New Haven (Connecticut): De Gruyter; p. 97–115.
   Google Scholar
• Quaedvlieg W, Kema GHJ, Groenewald JZ, Verkley GJM, Seifbarghi S, Razavi M, Mirzadi-Gohari A, Mehrabi R, Crous PW. 2011. Zymoseptoria gen. nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts. Persoonia. 26:57–69.
   PubMed Web of Science ®Google Scholar
• Ranelli LB, Hendricks WQ, Lynn JS, Kivlin SN, Rudgers JA. 2015. Biotic and abiotic predictors of fungal colonization in grasses of the Colorado Rockies. Divers Distrib. 21:962–76.
   Web of Science ®Google Scholar
• Redman R, Sheehan KB, Stout RG, Rodriguez RJ, Henson JM. 2002. Thermo tolerance generated by plant/fungal symbiosis. Science. 298:1581.
   PubMed Web of Science ®Google Scholar
• Riddell WD. 1950. Permanent stained mycological preparations obtained by slide culture. Mycologia. 42:265–70.
   Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–74.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MRBAYES 3.2: efficient Bayesian phylogenetic inference and model selection across a large model space. Syst Biol. 61:539–42.
   PubMed Web of Science ®Google Scholar
• Rudgers JA, Fox S, Porras-Alfaro A, Herrera J, Kent D, Souza L, Chung YA, Jumpponen A. 2021. Data from: biogeography of root fungi in grasslands ver 2 [dataset]. Environ Data Initiative. Sept 30. accessed 2021 Nov 22. doi:https://doi.org/10.6073/pasta/3f63cf15ed0851494a79ba13761cd236.
   Google Scholar
• Rudgers JA, Fox S, Porras-Alfaro A, Herrera J, Reazin C, Kent DR, Souza L, Chung A, Jumpponen A. 2022. Biogeography of root-associated fungi in foundation grasses of North American Plains. J Biogeogr. 49:22–37.
   Web of Science ®Google Scholar
• Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W; Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A. 109:6241–46.
   PubMed Web of Science ®Google Scholar
• Silvestro D, Michalak I. 2012. raxmlGUI: a graphical frontend for RAxML. Org Divers Evol. 12:335–37.
   Web of Science ®Google Scholar
• Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 31:3210–12.
   PubMed Web of Science ®Google Scholar
• Simmons EG. 1990. Embellisia and related teleomorphs. Mycotaxon. 38:251–65.
   Web of Science ®Google Scholar
• Simmons MP, Ochoterena H, Carr TG. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence based phylogenetic analysis. Syst Biol. 50:454–62.
   PubMed Web of Science ®Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30:1312–13.
   PubMed Web of Science ®Google Scholar
• Stanke M, Steinkamp R, Waack S, Morgenstern B. 2004. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32:309–12.
   PubMed Web of Science ®Google Scholar
• Tanaka K, Hirayama K, Yonezawa H, Sato G, Toriyabe A, Kudo H, Hashimoto A, Matsumura M, Harada Y, Kurihara Y. 2015. Revision of the Massarineae (Pleosporales, Dothideomycetes). Stud Mycol. 82:75–136.
   Web of Science ®Google Scholar
• Vieira B, Barreto R. 2010. Liquid culture production of chlamydospores of Lewia chlamidosporiformans (Ascomycota: pleosporales), a mycoherbicide candidate for wild poinsettia. Australas Plant Pathol. 39:154–60.
   Web of Science ®Google Scholar
• White TJ, Bruns T, Lee S, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. New York, NY: Academic Press; p. 315–22.
   Google Scholar
• Wickham H. 2016. ggplot 2: elegant graphics for data analysis. New York (New York): Springer-Verlag.
   Google Scholar
• Xu L, Bao D-F, Luo Z-L, Su X-J, Shen H-W, Su H-Y. 2020. Lignicolous freshwater ascomycota from Thailand: phylogenetic and morphological characterisation of two new freshwater fungi: tingoldiago hydei sp. nov. and T. clavata sp. nov. from Eastern Thailand. MycoKeys. 65:119–38.
   Web of Science ®Google Scholar
• Young ND, Healy J. 2003. GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinform. 4:6.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Crous P, Schoch C, Hyde K. 2012. Pleosporales. Fungal Divers. 53:1–221.
   PubMed Web of Science ®Google Scholar