Agriculture 2022, 12, 255. https://doi.org/10.3390/agriculture12020255 www.mdpi.com/journal/agriculture Article Pathogenic Interactions between Macrophomina phaseolina and Magnaporthiopsis maydis in Mutually Infected Cotton Sprouts Ofir Degani 1,2, *, Paz Becher 1,2 and Asaf Gordani 1,2 1 Plant Sciences Department, Migal—Galilee Research Institute, Tarshish 2, Kiryat Shmona 11016, Israel; pazbec@gmail.com (P.B.); asigordani1@gmail.com (A.G.) 2 Faculty of Sciences, Tel-Hai College, Upper Galilee, Tel-Hai 12210, Israel * Correspondence: d-ofir@bezeqint.net or ofird@telhai.ac.il; Tel.: +972-54-678-0114 Abstract: The soil fungus Macrophomina phaseolina, the charcoal rot disease agent, poses a major threat to cotton fields. In Israel, highly infected areas are also inhabited by the maize pathogen Mag- naporthiopsis maydis. This study reveals the relationships between the two pathogens and their im- pact on cotton sprouts. Infecting the soil 14 days before sowing (DBS) with each pathogen or with M. phaseolina before M. maydis caused a strong inhibition (up to 50–65%) of the sprouts’ development and survival, accompanied by each pathogen’s high DNA levels in the plants. However, combined or sequence infection with M. maydis first led to two distinct scenarios. This pathogen acted as a beneficial protective endophyte in one experiment, leading to significantly high emergence and growth indices of the plants and a ca. 10-fold reduction in M. phaseolina DNA in the sprouts’ roots. In contrast, M. maydis showed strong virulence potential (with 43–69% growth and survival sup- pression) in the other experiment, proving its true nature as an opportunist. Interestingly, soil inoc- ulation with M. phaseolina first, 14 DBS (but not at sowing), shielded the plants from M. maydis’ devastating impact. The results suggest that the two pathogens restrict each other, and this equilib- rium may lead to a moderate disease burst. Keywords: Cephalosporium maydis; charcoal rot disease; cotton; crop protection; fungus; Harpophora maydis; late wilt; maize; microflora; real-time PCR 1. Introduction Plants are threatened by a diversity of pathogen species living in complex communi- ties, including also a variety of other non-pathogenic microorganisms. A plant’s pathobi- omes can be defined as a collection of coexisting phytopathogens that affect each other and the plant [1]. They are formed by pathogens inhabiting the same ecological niche and either cooperating or competing for the same plant resources. Two or more phytopatho- gens on the same host can result in significantly different disease outcomes compared to single infections [2]. The communities of natural microorganisms inhabiting the plant phyllosphere, the aboveground portions of the plant’s habitat, or the rhizosphere, the roots’ surrounding habitat, also include non-pathogenic members that can have protec- tive effects against pathogens. For example, it has been shown lately that maize (Zea mays) grains are populated with a diversity of fungi and bacteria [3], some of which are known phytopathogens such as Alternaria alternata and Fusarium proliferatum, which can be op- portunists, causing disease when the conditions are favorable. Other members of the maize grains’ microflora are beneficial bioprotective species, including the fungal species T. asperellum, Penicillium citrinum, Chaetomium cochliodes, and the bacteria Bacillus subtilis. Citation: Degani, O.; Becher, P.; Gordani, A. Pathogenic Interactions between Macrophomina phaseolina and Magnaporthiopsis maydis in Mutually Infected Cotton Sprouts. Agriculture 2022, 12, 255. https://doi.org/10.3390/ agriculture12020255 Academic Editor: Ana Isabel López-Sesé Received: 16 January 2022 Accepted: 8 February 2022 Published: 10 February 2022 Publisher’s Note: MDPI stays neu- tral with regard to jurisdictional claims in published maps and institu- tional affiliations. Copyright: © 2022 by the authors. Li- censee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and con- ditions of the Creative Commons At- tribution (CC BY) license (http://crea- tivecommons.org/licenses/by/4.0/).