Burki, F. The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb Perspect. Biol. 6, a016147 (2014).
Beakes, G. W., Glockling, S. L. & Sekimoto, S. The evolutionary phylogeny of the Oomycota fungi. Protoplasma 249, 3–19 (2012).
Beakes, G. W. & Thines, M. Hyphochytriomycota and Oomycota in Handbook of the Protists (eds. Archibald, J. M., Simpson, A. G. B. & Slamovits, C. H.) 435–505 (Springer, 2017).
Svoboda, J., Mrugała, A., Kozubíková-Balcarová, E. & Petrusek, A. Hosts and transmission of the crayfish plague pathogen Aphanomyces astaci: a review. J. Fish. Dis. 40, 127–140 (2017).
Lone, S. A. & Manohar, S. Saprolegnia parasitica, a lethal Oomycota pathogen: demands to be controlled. J. Infect. Mol. Biol. 6, 36–44 (2018).
Czeczuga, B., Kozłowska, M. & Godlewska, A. Zoosporic aquatic fungi growing on dead specimens of 29 freshwater crustacean species. Limnologica 32, 180–193 (2002).
Steciow, M. M. The occurrence of Achlya recurva (Saprolegniales, Oomycota) in hydrocarbon-polluted soil from Argentina. Rev. Iberoam Micol. 14, 135–137 (1997).
Inaba, S. & Tokumasu, S. Saprolegnia semihypogyna sp. nov., a saprolegniaceous Oomycota isolated from soil in Japan. Mycoscience 43, 73–76 (2002).
Gaulin, E., Jacquet, C., Bottin, A. & Dumas, B. Root rot disease of legumes caused by Aphanomyces euteiches. Mol. Plant. Pathol. 8, 539–548 (2007).
Lévesque, C. A. et al. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 11, 1–22 (2010).
Fry, W. Phytophthora infestans: the plant (and R gene) destroyer. Mol. Plant. Pathol. 9, 385–402 (2008).
El-Hissy, F. T., Khallil, A. M. & El-Nagdy, M. A. Fungi associated with some aquatic plants collected from freshwater areas at Assiut (upper Egypt). J. Islam Acad. Sci. 3, 298–304 (1990).
Uzuhashi, S., Okada, G. & Ohkuma, M. Four new Pythium species from aquatic environments in Japan. Antonie Van Leeuwenhoek. 107, 375–391 (2015).
Nam, B. & Choi, Y. J. Phytopythium and Pythium species (Oomycota) isolated from freshwater environments of Korea. Mycobiology 47, 261–272 (2019).
Sparrow, F. K. Aquatic Phycomycetes (University of Michigan Press, 1960).
Johnson, T. W., Seymour, R. L. & Padgett, D. E. Biology and systematics of the Saprolegniaceae (2002).
Mahadevakumar, S. & Sridhar, K. R. Diagnosis of Pythium by classical and molecular approaches in Pythium: Diagnosis, Diseases and Management (eds. Rai, M., Abd-Elsalam, K. A. & Ingle, A. P.) 200–224 (CRC Press, 2020).
Rossmann, S., Lysøe, E., Skogen, M., Talgø, V. & Brurberg, M. B. DNA metabarcoding reveals broad presence of plant pathogenic Oomycota in soil from internationally traded plants. Front. Microbiol. 12, 637068 (2021).
Savian, F., Marroni, F., Ermacora, P., Firrao, G. & Martini, M. A metabarcoding approach to investigate fungal and Oomycota communities associated with Kiwifruit vine decline syndrome in Italy. Phytobiomes J. 6, 290–304 (2022).
Redekar, N. R., Eberhart, J. L. & Parke, J. L. Diversity of Phytophthora, Pythium, and Phytopythium species in recycled irrigation water in a container nursery. Phytobiomes J. 3, 31–45 (2019).
Jiang, R. H. Y. & Tyler, B. M. Mechanisms and evolution of virulence in Oomycota. Annu. Rev. Phytopathol. 50, 295–318 (2012).
Jiang, R. H. Y. et al. Distinctive expansion of potential virulence genes in the genome of the Oomycota fish pathogen Saprolegnia parasitica. PLoS Genet. 9, e1003272 (2013).
Fiore-Donno, A. M. & Bonkowski, M. Different community compositions between obligate and facultative Oomycota plant parasites in a landscape-scale metabarcoding survey. Biol. Fertil. Soils. 57, 245–256 (2021).
Nechwatal, J., Wielgoss, A. & Mendgen, K. Diversity, host, and habitat specificity of Oomycota communities in declining Reed stands (Phragmites australis) of a large freshwater lake. Mycol. Res. 112, 689–696 (2008).
Wielgoss, A., Nechwatal, J., Bogs, C. & Mendgen, K. Host plant development, water level and water parameters shape Phragmites australis-associated Oomycota communities and determine Reed pathogen dynamics in a large lake. FEMS Microbiol. Ecol. 69, 255–265 (2009).
Sakaguchi, S. O. et al. Molecular identification of water molds (Oomycota) associated with Chum salmon eggs from hatcheries in Japan and possible sources of their infection. Aquac Int. 27, 1739–1749 (2019).
Ahadi, R., Bouket, A. C., Alizadeh, A., Masigol, H. & Grossart, H. P. Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments. Sci. Rep. 14, 31701 (2024).
Abdelzaher, H. M. A., Ichitani, T. & Elnaghy, M. A. Virulence of Pythium spp. isolated from pond water. Mycoscience 35, 429–432 (1994).
Kageyama, K. et al. Plant Pathogenic Oomycota Inhabiting River Water Are a Potential Source of Infestation in Agricultural Areas in River Basin Environment: Evaluation, Management and Conservation (eds. Li, F., Awaya, Y., Kageyama, K. & Wei, Y.) 261–288 (Springer, 2022).
Schenk, A. Algologische Mittheilungen. Verh Phys. Med. Ges Würzbg. 9, 12–31 (1859).
Vanterpool, T. C. & Ledingham, G. A. Studies on “browning” root rot of cereals: I. The association of Lagena radicicola n. gen.; n. sp., with root injury of wheat. Can. J. Res. 2, 171–194 (1930).
Truscott, J. H. L. Observations on Lagena radicicola. Mycologia 25, 263–265 (1933).
Macfarlane, I. Lagena radicicola and Rhizophydium graminis, two common and neglected fungi. Trans. Br. Mycol. Soc. 55, 113–416 (1970).
Cerri, M. et al. Oomycota communities associated with Reed die-back syndrome. Front. Plant. Sci. 8, 1550 (2017).
Thines, M. & Buaya, A. T. Lagena—an overlooked Oomycota genus with a wide range of hosts. Mycol. Prog. 21, 66 (2022).
Van West, P. Saprolegnia parasitica, an Oomycota pathogen with a fishy appetite: new challenges for an old problem. Mycologist 20, 99–104 (2006).
Masigol, H. et al. Advancements, deficiencies, and future necessities of studying Saprolegniales: A semi-quantitative review of 1073 published papers. Fungal Biol. Rev. 46, 100319 (2023).
Hulvey, J. P., Padgett, D. E. & Bailey, J. C. Species boundaries within Saprolegnia (Saprolegniales, Oomycota) based on morphological and DNA sequence data. Mycologia 99, 421–429 (2007).
Pires-Zottarelli, C. L. A., de Oliveira Da Paixão, S. C., da Silva Colombo, D. R., Boro, M. C. & de Jesus, A. L. Saprolegnia atlantica sp. nov. (Oomycota, Saprolegniaceae) from Brazil, and new synonymizations and epitypifications in the genus Saprolegnia. Mycol. Prog. 21, 41 (2022).
Grossart, H. P. et al. Top-down and bottom‐up induced shifts in bacterial abundance, production and community composition in an experimentally divided humic lake. Environ. Microbiol. 10, 635–652 (2008).
Scholtysik, G. et al. Geochemical focusing and sequestration of manganese during eutrophication of lake Stechlin (NE Germany). Biogeochemistry 151, 313–334 (2020).
Perkins, A. K. et al. Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany. Fungal Ecol. 41, 116–125 (2019).
Allgaier, M. & Grossart, H. P. Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in Northeastern Germany. Aquat. Microb. Ecol. 45, 115–128 (2006).
Pavić, D. et al. Variations in the sporulation efficiency of pathogenic freshwater Oomycota in relation to the Physico-Chemical properties of natural waters. Microorganisms 10, 520 (2022).
Meinelt, T. et al. Reduction in vegetative growth of the water mold Saprolegnia parasitica (Coker) by humic substance of different qualities. Aquat. Toxicol. 83, 93–103 (2007).
Masigol, H. et al. The contrasting roles of aquatic fungi and Oomycota in the degradation and transformation of polymeric organic matter. Limnol. Oceanogr. 64, 2662–2678 (2019).
Masigol, H. et al. Phylogenetic and functional diversity of Saprolegniales and Fungi isolated from temperate lakes in Northeast Germany. J. Fungi. 7, 968 (2021).
Semenov, M. V. Metabarcoding and metagenomics in soil ecology research: achievements, challenges, and prospects. Biol. Bull. Rev. 11, 40–53 (2021).
Auer, L. et al. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. New. Phytol. 242, 1676–1690 (2024).
Schlatter, D. C., Burke, I. & Paulitz, T. C. Succession of fungal and Oomycota communities in glyphosate-killed wheat roots. Phytopathology 108, 582–594 (2018).
Dickie, I. A. et al. Oomycota along a 120,000 year temperate rainforest ecosystem development chronosequence. Fungal Ecol. 39, 192–200 (2019).
Lang-Yona, N. et al. Species richness, rRNA gene abundance, and seasonal dynamics of airborne plant-pathogenic Oomycota. Front. Microbiol. 9, 2673 (2018).
da Silva, N. J. et al. Spatio-temporal drivers of different Oomycota beta diversity components in Brazilian rivers. Hydrobiologia 848, 4695–4712 (2021).
Masigol, H., Mostowfizadeh-Ghalamfarsa, R. & Grossart, H. P. The current status of Saprolegniales in Iran: calling mycologists for better taxonomic and ecological resolutions. Mycol. Iran. 8, 1–13 (2021).
Wang, Q. & Wang, X. Comparison of methods for DNA extraction from a single chironomid for PCR analysis. Pak J. Zool. 44, 421–426 (2012).
Schloss, P. D. et al. Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L. & Graf, J. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS One. 9, e94249 (2014).
Uzuhashi, S., Kakishima, M. & Tojo, M. Phylogeny of the genus Pythium and description of new genera. Mycoscience 51, 337–365 (2010).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020). https://www.R-project.org
Weiner, J. riverplot: Sankey or Ribbon Plots. R package version 0.10. (2021). https://CRAN.R-project.org/package=riverplot
Freudenthal, J., Dumack, K., Schaffer, S., Schlegel, M. & Bonkowski, M. Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes. The ISME Journal 18(1), p.wrae206 (2024).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Hsieh, T. C., Ma, K. H. & Chao, A. Interpolation and extrapolation for species diversity. R Package Version 2.0.20 (2020). http://chao.stat.nthu.edu.tw/wordpress/software-download
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.6-4. (2022). https://CRAN.R-project.org/package=vegan
Chen, H. VennDiagram: Generate High-Resolution Venn and Euler Plots. R package version 1.7.3. (2022). https://CRAN.R-project.org/package=VennDiagram
Love, M. I., Huber, W. & Anders, S. Moderated Estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
Foster, Z. S. L., Sharpton, T. J., Grünwald, N. J. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput. Biol. 13, e1005404 (2017).
Smither, M. L. & Jones, A. L. Pythium species associated with sour Cherry and the effect of P. irregulare on the growth of Mahaleb Cherry. Can. J. Plant. Pathol. 11, 1–8 (1989).
Masigol, H. et al. Notes on Dictyuchus species (Stramenopila, Oomycota) from Anzali lagoon, Iran. Mycol. Iran. 5, 79–89 (2018).
Walsh, P.S., Metzger, D.A. and Higuchi, R., 2013. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques, 54, 134–139 (2013).
White, T.J., Bruns, T., Lee, S.J.W.T. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics in PCR protocols: a guide to methods and applications (ed. Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J.) 315–322 (Academic Press, 1990).
Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids Symp. Ser. 41, 95–98 (1999).
De Cock, A. et al. Phytopythium: molecular phylogeny and systematics. Persoonia-Molecular Phylogeny Evol. Fungi. 34, 25–39 (2015).
Jankowiak, R., Stepniewska, H. & Bilanski, P. Notes on some Phytopythium and Pythium species occurring in oak forests in Southern Poland. Acta Mycol. 50, 1052 (2015).
Katoh, K., Rozewicki, A. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166 (2019).
Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).
Silvestro, D. & Michalak, I. RaxmlGUI: a graphical front-end for RAxML. Org. Divers. Evol. 12, 335–337 (2012).
