02431nas a2200121 4500008004100000245008400041210006900125490001200194520199600206100001802202700001802220856007102238 2015 eng d00aMutualism-parasitism paradigm synthesized from results of root-endophyte models0 aMutualismparasitism paradigm synthesized from results of rootend0 v5: e7763 a

Plant tissues host a variety of fungi. One important group is the dark septate endophytes (DSEs) that colonize plant roots and form characteristic intracellular structures – melanized hyphae and microsclerotia. The DSE associations are common and frequently observed in various biomes and plant taxa. Reviews suggest that the proportion of plant species colonized by DSE equal that colonized by AM and microscopic studies show that the proportion of the root system colonized by fungi DSE can equal, or even exceed, the colonization by AM fungi. Despite the high frequency and suspected ecological importance, the effects of DSE colonization on plant growth and performance have remained unclear. Here, we draw from over a decade of experimentation with the obscure DSE symbiosis and synthesize across large bodies of published and unpublished data from Arabidopsis thaliana and Allium porrum model systems as well as from experiments that use native plants to better resolve the host responses to DSE colonization. The data indicate similar distribution of host responses in model and native plant studies, validating the use of model plants for tractable dissection of DSE symbioses. The available data also permit empirical testing of the environmental modulation of host responses to DSE colonization and refining the “mutualism-parasitism-continuum” paradigm for DSE symbioses. These data highlight the context dependency of the DSE symbioses: not only plant species but also ecotypes vary in their responses to populations of conspecific DSE fungi – environmental conditions further shift the host responses similar to those predicted based on the mutualism-parasitism-continuum paradigm. The model systems provide several established avenues of inquiry that permit more detailed molecular and functional dissection of fungal endophyte symbioses, identifying thus likely mechanisms that may underlie the observed host responses to endophyte colonization.

1 aMandyam, K.G.1 aJumpponen, A. uhttps://www.frontiersin.org/articles/10.3389/fmicb.2014.00776/full01785nas a2200157 4500008004100000245008900041210006900130260002800199300001300227520125100240100001801491700001801509700001601527700001601543856006801559 2014 eng d00aUnraveling the dark septate endophyte functions: insights from the Arabidopsis model0 aUnraveling the dark septate endophyte functions insights from th bSpringer-Verlag, Berlin a115 -1413 a

The global occurrence of plant root-associated fungal endophytes and their great abundance in many habitats necessitate studies to decipher their potential functions. Improved understanding of the basic endophyte ecology including host range, host preference, and host responses to endophyte colonization has been made possible through populations of endophytes (e.g., Periconia macrospinosa and Microdochium sp.) isolated from North American native tallgrass prairie. The recent demonstration of the endophyte symbiosis of the model plant Arabidopsis thaliana has provided additional tools to further elucidate the ecology of these endophytes. The availability of a large number of Arabidopsis ecotypes and mutants, microarrays, and databases allows the molecular dissection of endophyte symbiosis to better understand the importance of fungal endophytes in host nutrient uptake, defenses, and/or responses to pathogens and stress. In this chapter, we discuss the ecology and functions of endophytic fungi through experiments utilizing the Arabidopsis model system. We draw parallels with another deeply dissected Piriformospora indica root endophyte symbiosis, which has been demonstrated to promote growth of model and non-model plants.

1 aMandyam, K.G.1 aJumpponen, A.1 aVerma, V.C.1 aGange, A.C. uhttps://link.springer.com/chapter/10.1007%2F978-81-322-1575-2_602009nas a2200169 4500008004100000245008000041210006900121260005800190300001300248520138600261100001801647700001801665700001801683700001601701700001701717856010501734 2013 eng d00aAdoption and utility of an Arabidopsis model to dissect endophyte symbioses0 aAdoption and utility of an Arabidopsis model to dissect endophyt aBraunschweigbDeutsche Phytomedizinische Gesellschaft a244 -2473 aDespite the abundance of root-associated endophytic fungi, their function has remained elusive. During experiments to determine the host ranges of common endophytes isolated from a tallgrass prairie, at least two taxa (Microdocchium and Periconia) were observed to form functional mutualisms with Arabidopsis thaliana and increase the host’s growth. Furthermore, these endophytes reduce A. thaliana susceptibility to a foliar pathogen suggesting induction of systemic plant defenses. Arabidopsis thaliana does not associate with mycorrhizal fungi and there are only limited examples of endophyte associations in A. thaliana. Accordingly, we have taken advantage of this unique and fortuitous mutualism to further our understanding of the root-associated symbioses. We argue that this system is broadly applicable and the wealth of information available for A. thaliana will allow advances in understanding mycorrhizal and non-mycorrhizal root symbioses alike. Data from unpublished and ongoing microarray (Affymetrix ATH1) experiments indicate that endophytes lead to upregulation of carbon metabolism as well as general plant defenses against potentially pathogenic fungi. Furthermore, metabolome level experiments indicate clear shifts on metabolic profiles. Together, these data indicate that both host transcriptome and metabolome are modulated by the endophyte symbionts. 1 aJumpponen, A.1 aMandyam, K.G.1 aSchneider, C.1 aLeifert, C.1 aFeldmann, F. uhttp://lter.konza.ksu.edu/content/adoption-and-utility-arabidopsis-model-dissect-endophyte-symbioses01943nas a2200193 4500008004100000245010200041210006900143300001300212490000800225520126600233653003401499653002101533653003701554653002701591100001801618700001201636700001801648856008301666 2013 eng d00aArabidopsis thaliana model system reveals a continuum of responses to root endophyte colonization0 aArabidopsis thaliana model system reveals a continuum of respons a250 -2600 v1173 a

We surveyed the non-mycorrhizal model plant Arabidopsis thaliana microscopically for its ability to form dark septate endophyte (DSE) symbioses in field, greenhouse, and laboratory studies. The laboratory studies were also used to estimate host growth responses to 34 Periconia macrospinosa and four Microdochium sp. isolates. Consistent with broad host range observed in previous experiments, field-, greenhouse-, and laboratory-grown A. thaliana were colonized by melanized inter- and intracellular hyphae and microsclerotia or chlamydospores indicative of DSE symbiosis. Host responses to colonization were variable and depended on the host ecotype. On average, two A. thaliana accessions (Col-0 and Cvi-0) responded negatively, whereas one (Kin-1) was unresponsive, a conclusion consistent with our previous analyses with forbs native to the field site where the fungi originate. Despite the average negative responses, examples of positive responses were also observed, a conclusion also congruent with earlier studies. Our results suggest that A. thaliana has potential as a model for more detailed dissection of the DSE symbiosis. Furthermore, our data suggest that host responses are controlled by variability in the host and endophyte genotypes.

10aDark septate endophytes (DSE)10aMicrodochium sp.10aMutualism–parasitism continuum10aPericonia macrospinosa1 aMandyam, K.G.1 aRoe, J.1 aJumpponen, A. uhttps://www.sciencedirect.com/science/article/pii/S1878614613000226?via%3Dihub02449nas a2200181 4500008004100000245010500041210006900146300001300215490000700228520182000235653003402055653003702089653002702126100001802153700001202171700001802183856006602201 2012 eng d00aSeptate endophyte colonization and host responses of grasses and forbs native to a tallgrass prairie0 aSeptate endophyte colonization and host responses of grasses and a109 -1190 v223 a

Native tallgrass prairies support distinct dark septate endophyte (DSE) communities exemplified by Periconia macrospinosa and Microdochium sp. that were recently identified as common root symbionts in this system. Since these DSE fungi were repeatedly isolated from grasses and forbs, we aimed to test their abilities to colonize different hosts. One Microdochium and three Periconia strains were screened for colonization and growth responses using five native grasses and six forbs in an in vitro system. Previously published data for an additional grass (Andropogon gerardii) were included and reanalyzed. Presence of indicative inter- and intracellular structures (melanized hyphae, microsclerotia, and chlamydospores) demonstrated that all plant species were colonized by the DSE isolates albeit to varying degrees. Microscopic observations suggested that, compared to forbs, grasses were colonized to a greater degree in vitro. Host biomass responses varied among the host species. In broad comparisons, more grass species than forbs tended to respond positively to colonization, whereas more forb species tended to be non-responsive. Based on the suspected differences in the levels of colonization, we predicted that tallgrass prairie grasses would support greater DSE colonization than forbs in the field. A survey of field-collected roots from 15 native species supported this hypothesis. Our study supports the “broad host range” of DSE fungi, although the differences in the rates of colonization in the laboratory and in the field suggest a greater compatibility between grasses and DSE fungi. Furthermore, host responses to DSE range from mutualism to parasitism, suggesting a genotype-level interplay between the fungi and their hosts that determines the outcome of this symbiosis.

10aDark septate endophytes (DSE)10aMutualism–parasitism continuum10aMycorrhizal dependency1 aMandyam, K.G.1 aFox, C.1 aJumpponen, A. uhttps://link.springer.com/article/10.1007%2Fs00572-011-0386-y02388nas a2200205 4500008004100000245012100041210006900162300001300231490000800244520163800252653003401890653001201924653001701936653002701953653001801980100001801998700001702016700001802033856013102051 2010 eng d00aIsolation and morphological and metabolic characterization of common endophytes in annually burned tallgrass prairie0 aIsolation and morphological and metabolic characterization of co a813 -8210 v1023 aDark septate endophytes (DSE) are common and abundant root-colonizing fungi in the native tallgrass prairie. To characterize DSE fungi were isolated from roots of mixed tallgrass prairie plant communities. Isolates were grouped according to morphology, and the grouping was refined by ITS-RFLP and/or sequencing of the ITS region. Sporulating species of Periconia, Fusarium, Microdochium and Aspergillus were isolated along with many sterile fungi. Leek resynthesis was used to quickly screen for DSE fungi among the isolates. Periconia macrospinosa and Microdochium sp. formed typical DSE structures in the roots; Periconia produced melanized intracellular microsclerotia in host root cortex, whereas Microdochium produced abundant melanized inter- and intracellular chlamydospores. To further validate the results of the leek resynthesis growth responses of leek and a dominant prairie grass, Andropogon gerardii, were assessed in a laboratory resynthesis system. Leek growth mainly was unresponsive to the inoculation with Periconia or Microdochium, whereas Andropogon tended to respond positively. Select Periconia and Microdochium isolates were tested further for their enzymatic capabilities and for ability to use organic and inorganic nitrogen sources. These fungi tested positive for amylase, cellulase, polyphenol oxidases and gelatinase. Periconia isolates used both organic and inorganic nitrogen sources. Our study identified distinct endophytes in a tallgrass prairie ecosystem and indicated that these endophytes can use a variety of complex nutrient sources, suggesting facultative biotrophic and saprotrophic habits.10aDark septate endophytes (DSE)10aenzymes10aMicrodochium10aPericonia macrospinosa10asterile fungi1 aMandyam, K.G.1 aLoughlin, T.1 aJumpponen, A. uhttp://lter.konza.ksu.edu/content/isolation-and-morphological-and-metabolic-characterization-common-endophytes-annually-burned00560nas a2200145 4500008004100000245008500041210006900126260002800195300001100223100001900234700001800253700001800271700001400289856011100303 2008 eng d00aDiversity, function and potential applications of the root-associated endophytes0 aDiversity function and potential applications of the rootassocia bSpringer-Verlag, Berlin a29 -591 aKageyama, S.A.1 aMandyam, K.G.1 aJumpponen, A.1 aVarma, A. uhttp://lter.konza.ksu.edu/content/diversity-function-and-potential-applications-root-associated-endophytes01760nas a2200181 4500008004100000245017400041210006900215300001300284490000700297520106400304653003101368653003401399653002001433653002301453100001801476700001801494856006601512 2008 eng d00aSeasonal and temporal dynamics of arbuscular mycorrhizal and dark septate endophytic fungi in a tallgrass prairie ecosystem are minimally affected by nitrogen enrichment0 aSeasonal and temporal dynamics of arbuscular mycorrhizal and dar a145 -1550 v183 a

Root colonization by arbuscular mycorrhizae (AM) and dark septate endophytic (DSE) fungi in nitrogen amended and unamended mixed tallgrass prairie communities were analyzed monthly over two growing seasons. Roots were stained with Trypan blue and Sudan IV and fungal structures quantified using the modified magnified intersections method. Root length colonized (RLC) by DSE exceeded AM colonization during early part of the growing season. Fungal colonization varied among the years and was greater in 2003 than in 2002. Seasonal variation among the months within a growing season was observed in 2002 but not in 2003 for both AM and DSE. AM fungi were most abundant during the peak growing season of dominant C4 vegetation while DSE were most abundant during the early part of the growing season. Hyperparasitism of AM hyphal coils by melanized septate fungi was frequently observed and increased with AM coil frequency. Although nitrogen amendment had altered the plant community composition, it had no impact on the colonization by AM or DSE fungi.

10aArbsucular mycorrhiza (AM)10aDark septate endophytes (DSE)10aHyperparasitism10aNitrogen amendment1 aMandyam, K.G.1 aJumpponen, A. uhttps://link.springer.com/article/10.1007%2Fs00572-008-0165-602819nas a2200193 4500008004100000245009000041210006900131300001300200490000700213520214500220653001402365653003402379653003002413653001402443653001502457100001802472700001802490856011702508 2005 eng d00aAbundance and possible functions of the root-colonising dark septate endophytic fungi0 aAbundance and possible functions of the rootcolonising dark sept a173 -1890 v533 aA comparison of published estimates of mycorrhizal and dark septate endophyte (DSE) colonisation from various ecosystems suggests that DSE may be as abundant as mycorrhizal fungi as judged by the proportion of host plants colonised in mixed plant communities, or by the extent of colonisation in sampled root systems. While many strides have been made in understanding the ecological significance of the mycorrhizal fungi, our knowledge about the role of DSE fungi is in its infancy. In order to provide a framework of testable hypotheses, we review and discuss the most likely functions of this poorly understood group of root-associated fungi. We propose that, like mycorrhizal symbioses, DSE-plant symbioses should be considered multifunctional and not limited to nutrient acquisition and resultant positive host growth responses. Admittedly, many mycorrhizal and endophyte functions, (e.g. stress tolerance, pathogen or herbivore deterrence) are likely to be mediated by improved nutritional status and increased fitness of the host. Accordingly, it is pivotal to establish whether or not the DSE fungi are involved in host nutrient acquisition, either from inorganic and readily soluble sources, or from organic and recalcitrant sources. Facilitation by DSE of the use of organic nitrogen, phosphorus and sulphur sources by plants is a topic that warrants further attention and research. Even in the absence of a clear nutrient uptake function, the extensive DSE colonisation that occurs is likely to pre-emptively or competitively deter pathogens by minimising the carbon available in host rhizosphere environment. The DSEs' high melanin levels and their potential production of secondary metabolites toxic or inhibitory to herbivores are also likely to be factors influencing host performance. Finally, the broad host ranges speculated for most DSE fungi thus far suggest that they are candidates for controlling plant community dynamics via differential host responses to colonisation. We emphasise the need for simple experiments that allow unravelling of the basic biological functions of DSE fungi when they colonise their hosts.10aabundance10aDark septate endophytes (DSE)10amultifunctional symbioses10amutualism10amycorrhiza1 aMandyam, K.G.1 aJumpponen, A. uhttp://lter.konza.ksu.edu/content/abundance-and-possible-functions-root-colonising-dark-septate-endophytic-fungi01760nas a2200205 4500008004100000245014500041210006900186300001300255490000700268520099200275653002601267653002401293653001801317653002201335100001801357700001901375700001801394700001801412856012401430 2005 eng d00aNitrogen enrichment causes minimal changes in arbuscular mycorrhizal colonization but shifts community composition - evidence from rDNA data0 aNitrogen enrichment causes minimal changes in arbuscular mycorrh a217 -2240 v413 aIntracellular arbuscular mycorrhizal (AM) colonization was compared between nitrogen (NH4NO3) fertilized (10 g N m−2) and nonfertilized tallgrass prairie plots. In the microscopic analyses of host roots, only intracellular coils showed an increasing trend as a result of N fertilization, whereas intracellular colonization by arbuscules, hyphae, or vesicles did not differ between the N treatments. Clone libraries established from pooled PCR products of AM fungi contained exclusively species of Glomus; no other genera were detected indicating that Glomus spp. dominated the host roots. Comparisons between observed and random topologies indicated that cloned sequence placement covaried with N treatment: unique clades within Glomus originated exclusively from N-fertilized or nonfertilized treatments. We conclude that the communities of dominant and most commonly occurring AM fungi changed in response to N amendment, although the root colonization showed minimal or no response.10aArbuscular mycorrhiza10aNitrogen deposition10aRibosomal DNA10atallgrass prairie1 aJumpponen, A.1 aTrowbridge, J.1 aMandyam, K.G.1 aJohnson, L.C. uhttp://lter.konza.ksu.edu/content/nitrogen-enrichment-causes-minimal-changes-arbuscular-mycorrhizal-colonization-shifts00573nas a2200121 4500008004100000245012900041210006900170260004300239300001000282490001400292100001800306856012700324 2004 eng d00aSeasonal and temporal variation of arbuscular mycorrhizal and dark septate endophytic fungi in a tallgrass prairie ecosystem0 aSeasonal and temporal variation of arbuscular mycorrhizal and da aManhattan, KSbKansas State University a1 -630 vMS Thesis1 aMandyam, K.G. uhttp://lter.konza.ksu.edu/content/seasonal-and-temporal-variation-arbuscular-mycorrhizal-and-dark-septate-endophytic-fungi