00773nas a2200193 4500008004500000245015400045210006900199100002200268700002500290700002300315700001800338700001600356700001600372700001900388700001700407700001400424700002200438856011900460 In Press eng d 00aPleoardoris graminearum gen. et sp. nov., a new member of Pleosporales from the North American Plains, biogeography and effects on B. gracilis growth0 aPleoardoris graminearum gen et sp nov a new member of Pleosporal1 aPinchi-Davila, X.1 aVargas-Hernandez, D.1 aRomero-Jimenez, M.1 aJumpponen, A.1 aRudgers, J.1 aHerrera, J.1 aHutchinson, M.1 aDunbar, J.M.1 aKuske, C.1 aPorras-Alfaro, A. uhttp://knz.lternet.edu/content/pleoardoris-graminearum-gen-et-sp-nov-new-member-pleosporales-north-american-plains00600nas a2200145 4500008004100000245014100041210006900182300001000251490000800261100001200269700001900281700001400300700001800314856012200332 2023 eng d00aAmorpha canescens and Andropogon gerardii recruit comparable foliar fungal communities across the steep precipitation gradient in Kansas0 aAmorpha canescens and Andropogon gerardii recruit comparable fol a31-500 v1261 aDea, H.1 aMcKenzie, D.A.1 aClark, B.1 aJumpponen, A. uhttp://knz.lternet.edu/content/amorpha-canescens-and-andropogon-gerardii-recruit-comparable-foliar-fungal-communities00619nas a2200121 4500008004100000245021300041210006900254260004300323490001400366100001200380700001800392856008700410 2023 eng d00aPrairie plant communities and their associated phyllosphere fungal communities change across the steep precipitation gradient in Kansas USA, though individual plant species’ phyllosphere communities may not0 aPrairie plant communities and their associated phyllosphere fung aManhattan, KSbKansas State University0 vMS Thesis1 aDea, H.1 aJumpponen, A. uhttps://krex.k-state.edu/bitstream/handle/2097/43453/HannahDea2023.pdf?sequence=1200630nas a2200205 4500008004100000245008900041210006900130300001000199490000700209100001800216700001200234700002200246700001600268700001500284700001500299700001400314700001600328700001800344856006200362 2022 eng d00aBiogeography of root-associated fungi in foundation grasses of North American plains0 aBiogeography of rootassociated fungi in foundation grasses of No a22-370 v491 aRudgers, J.A.1 aFox, S.1 aPorras-Alfaro, A.1 aHerrera, J.1 aReazin, C.1 aKent, D.R.1 aSouza, L.1 aChung, Y.A.1 aJumpponen, A. uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.1426000743nas a2200217 4500008004100000245012000041210006900161300001100230490000600241100002000247700001900267700001900286700002600305700002500331700001800356700002400374700002200398700001500420700001800435856007200453 2022 eng d00aPrecipitation, not land use, primarily determines the composition of both plant and phyllosphere fungal communities0 aPrecipitation not land use primarily determines the composition  a8052250 v31 aDea, Hannah, I.1 aUrban, Abigail1 aKazarina, Anna1 aHouseman, Gregory, R.1 aThomas, Samantha, G.1 aLoecke, Terry1 aGreer, Mitchell, J.1 aPlatt, Thomas, G.1 aLee, Sonny1 aJumpponen, A. uhttps://www.frontiersin.org/articles/10.3389/ffunb.2022.805225/full00736nas a2200217 4500008004100000245011000041210007300151300001400224490000800238100001900246700001800265700002200283700001800305700001600323700002100339700001800360700002000378700001800398700002600416856007600442 2021 eng d00aExperimental drought re‐ordered assemblages of root‐associated fungi across North American grasslands0 aExperimental drought re‐ordered assemblages of root‐associated f a776 - 7920 v1091 aLagueux, Devon1 aJumpponen, A.1 aPorras-Alfaro, A.1 aHerrera, Jose1 aChung, Anny1 aBaur, Lauren, E.1 aSmith, M., D.1 aKnapp, Alan, K.1 aCollins, S, L1 aRudgers, Jennifer, A. uhttps://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2745.1350502228nas a2200157 4500008004100000245015200041210006900193300001100262490000700273520165000280100002201930700001701952700001601969700001801985856006702003 2021 eng d00aSoil fungal communities are compositionally resistant to drought manipulations – Evidence from culture-dependent and culture-independent analyses0 aSoil fungal communities are compositionally resistant to drought a1010620 v513 a

Current environmental change predictions forecast intensified drought conditions. It is becoming increasingly evident that plant communities are sensitive to drought and that soil-inhabiting microbial communities vary along precipitation gradients. However, the drought sensitivity of microbial communities in general and that of soil fungi in particular remains unclear, even though understanding their responses to adverse environmental conditions is vital for better understanding of ecosystem service provisioning. We sampled soils at two sites with established experiments that imposed extreme, chronic drought to assess fungal community responses. We analyzed fungal communities using both culture-dependent and -independent tools and MiSeq-sequenced communities from colony forming units (CFU-PCR) on a drought simulating medium and from environmental DNA (ePCR), to compare the conclusions derived from these two methods. Our data from the two approaches consistently indicate that the composition of fungal communities is not affected by the drought treatment, whereas – based on the CFU-PCR but not ePCR data – their richness and diversity increased under drought conditions at the more mesic of the two sites. Further, based on the direct comparisons of CFU-PCR and ePCR, we estimate that more than 10% of the fungal community and more than 20% of the ascomycetes were culturable. We conclude that although recent research indicates that plant and bacterial communities respond to drought, fungal community responses are more variable, particularly in experiments that impose chronic drought under field conditions.

1 aNarayanan, Achala1 aIsmert, K.J.1 aSmith, M.D.1 aJumpponen, A. uhttps://linkinghub.elsevier.com/retrieve/pii/S175450482100024600685nas a2200169 4500008004100000245016300041210006900204300001200273490000700285100001600292700002100308700001300329700001800342700001700360700001800377856012000395 2021 eng d00aWatershed and fire severity are stronger determinants of soil chemistry and microbiomes than within-watershed woody encroachment in a tallgrass prairie system0 aWatershed and fire severity are stronger determinants of soil ch afiab1540 v971 aMino, Laura1 aKolp, Matthew, R1 aFox, Sam1 aReazin, Chris1 aZeglin, L.H.1 aJumpponen, A. uhttps://academic.oup.com/femsec/advance-article-abstract/doi/10.1093/femsec/fiab154/6445025?redirectedFrom=fulltext02250nas a2200349 4500008004100000245011000041210006900151300001400220490000700234520126000241100001801501700001701519700001601536700001601552700001501568700001701583700001601600700002001616700001601636700001801652700001501670700001701685700001601702700001601718700001901734700001801753700001701771700001601788700001401804700001701818856006501835 2020 eng d00aConnections and feedback: Aquatic, plant, and soil microbiomes in heterogeneous and changing environments0 aConnections and feedback Aquatic plant and soil microbiomes in h a548 - 5620 v703 a

Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.

1 aDodds, W., K.1 aZeglin, L.H.1 aRamos, R.J.1 aPlatt, T.G.1 aPandey, A.1 aMichaels, T.1 aMasigol, M.1 aKlompen, A.M.L.1 aKelly, M.C.1 aJumpponen, A.1 aHauser, E.1 aHansen, P.M.1 aGreer, M.J.1 aFattahi, N.1 aDelavaux, C.S.1 aConnell, R.K.1 aBillings, S.1 aBever, J.D.1 aBarua, N.1 aAgusto, F.B. uhttps://academic.oup.com/bioscience/article/70/7/548/582695803052nas a2200205 4500008004100000245011900041210006900160300001100229490000700240520235700247100002602604700002202630700002102652700001802673700002702691700002402718700001902742700002402761856006102785 2020 eng d00aRepeated fire shifts carbon and nitrogen cycling by changing plant inputs and soil decomposition across ecosystems0 aRepeated fire shifts carbon and nitrogen cycling by changing pla ae014090 v903 a

Fires shape the biogeochemistry and functioning of many ecosystems, and fire frequencies are changing across much of the globe. Frequent fires can change soil carbon (C) and nitrogen (N) storage by altering the quantity and chemistry of plant inputs through changes in plant biomass and composition as well as altering decomposition of soil organic matter. How decomposition rates change with shifting inputs remains uncertain because most studies focus on the effects of single fires, where transient changes may not reflect responses to decadal changes in burning frequencies. Here, we sampled seven sites exposed to different fire frequencies. In four of the sites, we intensively sampled both soils and plant communities across four ecosystems in North America and Africa spanning tropical savanna, temperate coniferous savanna, temperate broadleaf savanna, and temperate coniferous forest ecosystems. Each site contained multiple plots burned frequently for 33‐61 years and nearby plots that had remained unburned over the same period replicated at the landscape scale. Across all sites, repeatedly burned plots had 25‐185% lower bulk soil C and N concentrations but also 2‐10‐fold lower potential decomposition of organic matter compared to unburned sites. Soil C and N concentrations and extracellular enzyme activities declined with frequent fire because fire reduced both plant biomass inputs into soils and dampened the localized enrichment effect of tree canopies. Examination of soil extracellular enzyme activities revealed that fire decreased the potential turnover of organic matter in the forms of cellulose, starch, and chitin (p<0.0001) but not polyphenol and lignin (p=0.09), suggesting a shift in soil C and N cycling. Inclusion of δ13C data from three additional savanna sites (19‐60 years of altered fire frequencies) showed that soil C losses were largest in sites where estimated tree inputs into soils declined the most (r2=0.91, p<0.01). In conclusion, repeated burning reduced C and N storage, consistent with previous studies, but fire also reduced potential decomposition, likely contributing to slower C and N cycling. Trees were important in shaping soil carbon responses across sites, but the magnitude of tree effects differed and depended on how tree biomass inputs into soil responded to fire.

1 aPellegrini, Adam.F.A.1 aHobbie, Sarah, E.1 aReich, Peter, B.1 aJumpponen, A.1 aBrookshire, E.N., Jack1 aCaprio, Anthony, C.1 aCoetsee, Corli1 aJackson, Robert, B. uhttps://onlinelibrary.wiley.com/doi/abs/10.1002/ecm.140900649nas a2200229 4500008004100000245006500041210006500106300001300171490000600184100001500190700001700205700001100222700001800233700001300251700001800264700001600282700001600298700001500314700001800329700001600347856005600363 2020 eng d00aTerabase metagenome sequencing of grassland soil microbiomes0 aTerabase metagenome sequencing of grassland soil microbiomes a00718-200 v91 aNelson, W.1 aAnderson, L.1 aWu, R.1 aMcDermott, J.1 aBell, S.1 aJumpponen, A.1 aFansler, S.1 aTyrrell, K.1 aFarris, Y.1 aHofmockel, K.1 aJansson, J. uhttps://mra.asm.org/content/9/32/e00718-20.abstract03041nas a2200373 4500008004100000245008800041210006900129300001400198490000600212520192100218653001602139653002202155653001602177653002002193100002702213700001902240700002102259700002402280700002602304700002102330700001802351700002302369700001802392700001802410700001702428700002302445700002102468700002002489700002702509700002002536700002302556700002302579856006502602 2019 eng d00aMetaphenomic response of a native prairie soil microbiome to moisture perturbations0 aMetaphenomic response of a native prairie soil microbiome to moi ae00061-190 v43 a

Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.

10ametaphenome10ametatranscriptome10amulti-omics10asoil microbiome1 aChowdhury, Taniya, Roy1 aLee, Joon-Yong1 aBottos, Eric, M.1 aBrislawn, Colin, J.1 aWhite, Richard, Allen1 aBramer, Lisa, M.1 aBrown, Joseph1 aZucker, Jeremy, D.1 aKim, Young-Mo1 aJumpponen, A.1 aRice, C., W.1 aFansler, Sarah, J.1 aMetz, Thomas, O.1 aMcCue, Lee, Ann1 aCallister, Stephen, J.1 aSong, Hyun-Seob1 aJansson, Janet, K.1 aHallam, Steven, J. uhttp://msystems.asm.org/lookup/doi/10.1128/mSystems.00061-1901712nas a2200157 4500008004100000245011500041210006900156300001200225490000700237520114100244100002601385700001801411700002001429700002201449856008301471 2019 eng d00aSoil fungal community changes in response to long-term fire cessation and N fertilization in tallgrass prairie0 aSoil fungal community changes in response to longterm fire cessa a45 - 550 v413 a

In grasslands, fire management and fertilization are established drivers of plant community change, but associated soil fungal responses are less well defined. We predicted that soil fungal communities would change seasonally, that decades of fire cessation and nitrogen (N) fertilization would alter fungal distributions, and that plant and fungal community change would be correlated. Surface soils were sampled monthly for 1 y from a 30-y fire by fertilization experiment to evaluate fungal community dynamics and assess correlation with plant community heterogeneity. ITS gene community composition was seasonally stable, excepting increased arbuscular mycorrhizal fungal summer abundance in the burned, fertilized treatment. Long-term treatments affected soil fungal and plant communities, with correlated heterogeneity patterns. Despite woody encroachment in the fire cessation treatment, soil fungal communities did not resemble those of forests. This study provides evidence supporting the strength of feedbacks between fungal and plant community change in response to long-term grassland fire and N management changes.

1 aCarson, Christine, M.1 aJumpponen, A.1 aBlair, John, M.1 aZeglin, Lydia, H. uhttps://www.sciencedirect.com/science/article/pii/S1754504818302538?via%3Dihub02509nas a2200157 4500008004100000245010900041210006900150300001200219490000700231520197000238100002302208700002302231700001802254700001802272856006102290 2018 eng d00aTop - down effects of a grazing, omnivorous minnow (Campostoma anomalum) on stream microbial communities0 aTop down effects of a grazing omnivorous minnow Campostoma anoma a121-1330 v373 a

Top–down control exerted by macroconsumers can strongly affect lower trophic levels and ecosystem processes. Studies of effects on primary consumers in streams have been focused on algae, and effects on bacteria are largely unknown. We manipulated the density of an omnivorous, grazing minnow, the central stoneroller (Campostoma anomalum), in experimental stream mesocosms (treatments with 0, 1, 2, 3, 4, 5, 6, or 7 individuals) to understand consumer effects on algal and bacterial abundance (chlorophyll a [Chl a] extraction, bacterial cell counts, biomass measurements) and bacterial diversity and community composition (via Illumina MiSeq sequencing of the V4 region of the 16S ribosomal RNA gene). Increasing C. anomalum density reduced algal biomass until density reached ~2 fish (5 g fish biomass/m2), and higher fish densities did not affect algal biomass. Fish biomass did not affect bacterial cell counts. Biofilm organic matter decreased with increasing C. anomalum biomass. Bacterial community composition was not affected by fish biomass, but variation in community composition was correlated with shifts in bacterial abundances. Evenness of bacterial operational taxonomic units (OTUs) decreased with increasing C. anomalum biomass, indicating that bacterial communities exhibited a greater degree of OTU dominance when fish biomass was higher. These findings suggest that this grazing fish species reduces algal abundance and organic matter in low-nutrient streams until a threshold of moderate fish abundance is reached and that it reduces evenness of benthic bacterial communities but not bacterial biomass. Given the importance of biofilm bacteria for ecosystem processes and the ubiquity of grazing fishes in streams, future researchers should explore both top–down and bottom–up interactions in alternative environmental contexts and with other grazing fish species.

1 aVeach, Allison, M.1 aTroia, Matthew, J.1 aJumpponen, A.1 aDodds, W., K. uhttps://www.journals.uchicago.edu/doi/abs/10.1086/69629202481nam a2200217 4500008004100000245009000041210006900131260004400200300001200244490000800256520178500264653001902049653002802068653001502096653001702111100001802128700001602146700002202162700001602184856006302200 2017 eng d00aBiogeography of root-associated endophytes. In: Biogeography of Mycorrhizal Symbiosis0 aBiogeography of rootassociated endophytes In Biogeography of Myc aChambSpringer International Publishing a195-2220 v2303 a

Healthy plant roots usually host heterogeneous communities of root endophytes that are abundant in all plants and ecosystems. Despite their abundance, current understanding of the distribution of these endophytes is superficial at the best. A comprehensive treatise of the distribution of variety of fungi described as root endophytes would most likely prove an exhausting exercise in futility, given the large gaps in current data. As a result, we broadly target the helotialean endophytes that are commonly observed in temperate and boreal, forested ecosystems and the pleosporalean endophytes commonly observed in grassland ecosystems. To explore the sparse data available for the distribution of these root-associated fungal endophytes, we combine references from current literature and a case study to evaluate whether or not the endophyte communities (1) shift over environmental gradients, (2) respond to some specific drivers, or (3) seem limited by dispersal by showing distance-decay responses. The data indicate that communities of endophytic fungi indeed change over large geographical scales. The available data suggest a Helotiales-dominated endophyte guild in forested ecosystems and a Pleosporales-dominated assemblage in grassland ecosystems. Further, large-scale studies and our preliminary analyses of communities across North American grassland ecosystems suggest some shifts corresponding to geographical/environmental gradients. However, specific drivers are difficult to distinguish because abiotic gradients are often correlated, resulting in complex model selection problems. Finally, we observed that our own and published data reach no agreement on distance decay, even though both agree that the distance decay may be of rather minor importance.

10aDistance decay10aEnvironmental filtering10aHelotiales10aPleosporales1 aJumpponen, A.1 aHerrera, J.1 aPorras-Alfaro, A.1 aRudgers, J. uhttps://link.springer.com/book/10.1007%2F978-3-319-56363-302397nas a2200169 4500008004100000245010300041210006900144300001600213490000700229520184400236100001602080700001702096700001602113700001802129700001802147856006202165 2016 eng d00aSpatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem0 aSpatial and successional dynamics of microbial biofilm communiti a4674 - 46880 v253 aBiofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third-order stream at Konza Prairie over a 2- to 64-day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta-, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early-stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.1 aVeach, A.M.1 aStagen, J.C.1 aBrown, S.P.1 aDodds, W., K.1 aJumpponen, A. uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/mec.1378403029nas a2200157 4500008004100000245009200041210006900133260004300202490002200245520236400267653008102631100001602712700001802728700001802746856010702764 2015 eng d00aDynamics of microbial community structure and function in a tallgrass prairie ecosystem0 aDynamics of microbial community structure and function in a tall aManhattan, KSbKansas State University0 vPhD. Dissertation3 a

Due to agricultural practices and urbanization, tallgrass prairie ecosystems have become threatened as < 5% of its historical coverage exists today. The small remainder of praire that does exist is further threatened by the encroachment of woody plant species. Woody plant encroachment may not only alter prairie ecosystem function, but also prairie microbial communities responsible for these functional processes. Further, prairies are high disturbance ecosystems, especially prairie streams which are hydrologically harsh. They support communities that frequently undergo succession due to recurring flood and drought conditions, yet little is known about the response of microbial communities to these disturbances. In my dissertation, I first address the degree of woody vegetation expansion in riparian corridors (parallel to streams) in watersheds with variable fire frequency and grazing. I found that the rate of riparian woody expansion declines with higher fire intervals and is not affected by grazing, but even annual burns may not prevent woody plant expansion in riparian zones from occurring. Second, I quantified the effect of using restorations of riparian corridors, through removal of woody plants, on physical, chemical, and microbial community (bacteria and fungi) dynamics across stream to upslope soils. Removal restoration causes a decrease in NH₄⁺ and soil water content, and causes streams and upslope soils to become similar in fungal community richness unlike forested landscapes. Bacterial communities were minimally impacted by removals, but were highly structured among stream to upslope soils due to multiple environmental gradients (i.e., pH, NO₃⁻, soil moisture). Lastly, I examined the successional development of biofilm-associated microbial communities in a prairie stream from both a functional and structural perspective. I found that biofilm microbes exhibited strong successional trajectories, with communities developing towards net autotrophy and therefore becoming reliant upon in-stream derived carbon. Further, bacterial communities displayed spatial differences, but much stronger temporal patterns in community composition were detected. These studies highlight how woody plant encroachment may influence stream ecosystems in addition to spatiotemporal trends in microbial community assembly.

10aMicrobial communities; Woody encroachment; Bacteria; Fungi; Biofilms; Stream1 aVeach, A.M.1 aDodds, W., K.1 aJumpponen, A. uhttp://krex.k-state.edu/dspace/bitstream/handle/2097/19145/AllisonVeach2015.pdf?sequence=1&isAllowed=y02431nas 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/full02088nas a2200253 4500008004100000245008500041210006900126300001300195490000700208520131900215653001001534653003101544653001901575653001401594100001601608700001601624700002201640700001401662700001901676700001701695700001701712700001801729856008701747 2015 eng d00aScraping the bottom of the barrel: are rare high throughput sequences artifacts?0 aScraping the bottom of the barrel are rare high throughput seque a221 -2250 v133 a

Metabarcoding data generated using next-generation sequencing (NGS) technologies are overwhelmed with rare taxa and skewed in Operational Taxonomic Unit (OTU) frequencies comprised of few dominant taxa. Low frequency OTUs comprise a rare biosphere of singleton and doubleton OTUs, which may include many artifacts. We present an in-depth analysis of global singletons across sixteen NGS libraries representing different ribosomal RNA gene regions, NGS technologies and chemistries. Our data indicate that many singletons (average of 38 % across gene regions) are likely artifacts or potential artifacts, but a large fraction can be assigned to lower taxonomic levels with very high bootstrap support (∼32 % of sequences to genus with ≥90 % bootstrap cutoff). Further, many singletons clustered into rare OTUs from other datasets highlighting their overlap across datasets or the poor performance of clustering algorithms. These data emphasize a need for caution when discarding rare sequence data en masse: such practices may result in throwing the baby out with the bathwater, and underestimating the biodiversity. Yet, the rare sequences are unlikely to greatly affect ecological metrics. As a result, it may be prudent to err on the side of caution and omit rare OTUs prior to downstream analyses.

10afungi10aHigh-throughput sequencing10aRare biosphere10aSingleton1 aBrown, S.P.1 aVeach, A.M.1 aRigdon-Huss, A.R.1 aGrond, K.1 aLickteig, S.K.1 aLothamer, K.1 aOliver, A.K.1 aJumpponen, A. uhttps://www.sciencedirect.com/science/article/abs/pii/S1754504814001068?via%3Dihub02188nas a2200217 4500008004100000245015900041210006900200260001600269300001100285490000700296520142400303653002601727653002301753653002701776653002201803653002301825100001601848700001801864700001801882856007001900 2015 eng d00aWoody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem0 aWoody plant encroachment and its removal impact bacterial and fu cDec-10-2015 afiv1090 v913 aWoody plant encroachment has become a global threat to grasslands and has caused declines in aboveground richness and changes in ecosystem function; yet we have a limited understanding on the effects of these phenomena on belowground microbial communities. We completed riparian woody plant removals at Konza Prairie Biological Station, Kansas and collected soils spanning land–water interfaces in removal and woody vegetation impacted areas. We measured stream sediments and soils for edaphic variables (C and N pools, soil water content, pH) and bacterial (16S rRNA genes) and fungal (ITS2 rRNA gene repeat) communities using Illumina MiSeq metabarcoding. Bacterial richness and diversity decreased with distance from streams. Fungal richness decreased with distance from the stream in wooded areas, but was similar across landscape position while Planctomycetes and Basidiomycota relative abundance was lower in removal areas. Cyanobacteria, Ascomycota, Chytridiomycota and Glomeromycota relative abundance was greater in removal areas. Ordination analyses indicated that bacterial community composition shifted more across land–water interfaces than fungi yet both were marginally influenced by treatment. This study highlights the impacts of woody encroachment restoration on grassland bacterial and fungal communities which likely subsequently affects belowground processes and plant health in this ecosystem.10abacterial communities10afungal communities10aland–water interface10atallgrass prairie10awoody encroachment1 aVeach, A.M.1 aDodds, W., K.1 aJumpponen, A. uhttp://femsec.oxfordjournals.org/lookup/doi/10.1093/femsec/fiv10901833nas a2200253 4500008004100000245012200041210006900163490001300232520105900245100001601304700001401320700001601334700001201350700001901362700001601381700002001397700001701417700001801434700001501452700001501467700001901482700001801501856006001519 2014 eng d00aFOAM: Functional Ontology Assignments for Metagenomes: a Hidden Markov Model (HMM) database with environmental focus0 aFOAM Functional Ontology Assignments for Metagenomes a Hidden Ma0 v42: e1453 a

A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.

1 aPrestat, E.1 aDavid, M.1 aHultman, J.1 aTas, N.1 aLamendella, R.1 aDvornik, J.1 aMackelprang, R.1 aMyrold, D.D.1 aJumpponen, A.1 aTringe, S.1 aHolman, E.1 aMavromatis, K.1 aJansson, J.K. uhttps://academic.oup.com/nar/article/42/19/e145/290247901942nas a2200181 4500008004100000245007800041210006900119300001100188490000700199520135100206653002601557653001901583653001501602653002201617100001801639700001601657856008701673 2014 eng d00aTallgrass prairie soil fungal communities are resilient to climate change0 aTallgrass prairie soil fungal communities are resilient to clima a44 -570 v103 a

Climate models for central United States predict increasing temperatures and greater variability in precipitation. Combined, these shifts in environmental conditions impact many ecosystem properties and services. Long-term climate change experiments, such as the Rainfall Manipulation Plots (RaMPs), can be used to address soil community responses to simultaneous manipulation of temperature and temporal variability in precipitation. The RaMPs experiment is located in a native tallgrass prairie at the Konza Prairie Biological Station and has been operational since 1998 providing the potential to address responses to long-term environmental manipulations. To test whether community composition, richness, or diversity respond to environmental change, more than 40 000 fungal amplicons were analyzed from soil samples collected in 2006. The data suggest that soil fungal communities are compositionally resilient to predicted environmental change. This is the case both for the community composition overall as inferred from ordination analyses as well as analyses of variance for each of the most common Operational Taxonomic Units (OTUs). However, while this study suggests compositional resilience, further studies are required to address functional attributes of these communities and their responses to environmental manipulations.

10aAltered precipitation10aGlobal warming10aSoil fungi10atallgrass prairie1 aJumpponen, A.1 aJones, K.L. uhttps://www.sciencedirect.com/science/article/abs/pii/S1754504813001141?via%3Dihub01785nas 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_602006nas a2200169 4500008004100000245008000041210006900121260005800190300001300248520138600261100001801647700001801665700001801683700001601701700001701717856010201734 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://knz.lternet.edu/content/adoption-and-utility-arabidopsis-model-dissect-endophyte-symbioses03323nas a2200217 4500008004100000245012400041210006900165300001500234490000700249520261700256100002202873700002002895700001802915700001702933700001502950700001702965700001602982700001602998700001703014856007403031 2013 eng d00aAltered precipitation regime affects the function and composition of soil microbial communities on multiple time scales0 aAltered precipitation regime affects the function and compositio a2334 -23450 v943 a

Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting “Ambient” and “Altered” (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = −0.01 and −0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 ± 0.03 > 0.46 ± 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (β-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal : bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet-up and between seasons and treatments. Overall, microbial activity may directly (C respiration) and indirectly (enzyme potential) reduce soil organic matter pools less in drier soils, and soil C sequestration potential (CUE) may be higher in soils with a history of extended dry periods between rainfall events. The implications include that soil C loss may be reduced or compensated for via different mechanisms at varying time scales, and that microbial taxa with better stress tolerance or growth efficiency may be associated with these functional shifts.

1 aZeglin, Lydia, H.1 aBottomley, P.J.1 aJumpponen, A.1 aRice, C., W.1 aArango, M.1 aLindsley, A.1 aMcGowan, A.1 aMfombep, P.1 aMyrold, D.D. uhttps://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/12-2018.101943nas 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%3Dihub00790nas a2200241 4500008004100000245009700041210006900138300001000207490000800217100001800225700002200243700001400265700001600279700001400295700001600309700001700325700001600342700001600358700001700374700001500391700001700406856012500423 2013 eng d00aFungal community responses to discrete precipitation pulses under altered rainfall intervals0 aFungal community responses to discrete precipitation pulses unde a182 -0 v1031 aJumpponen, A.1 aZeglin, Lydia, H.1 aDavid, M.1 aPrestat, E.1 aBrown, S.1 aDvornik, J.1 aLothamer, K.1 aHettich, R.1 aJansson, J.1 aRice, C., W.1 aTringe, S.1 aMyrold, D.D. uhttp://knz.lternet.edu/content/fungal-community-responses-discrete-precipitation-pulses-under-altered-rainfall-intervals02449nas 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-y01612nas a2200169 4500008004100000245010400041210006900145300001300214490000700227520104600234653001601280653001801296653002201314653002201336100001801358856006601376 2011 eng d00aAnalysis of ribosomal RNA indicates seasonal fungal community dynamics in Andropogon gerardii roots0 aAnalysis of ribosomal RNA indicates seasonal fungal community dy a453 -4640 v213 a

Use of the reverse-transcribed small subunit of the ribosomal RNA (rRNA) was tested for exploring seasonal dynamics of fungal communities associated with the roots of the dominant tallgrass prairie grass, Andropogon gerardii. Ribosomal RNA was extracted, reverse-transcribed, and PCR-amplified in four sampling events in May, July, September, and November. Analyses of cloned PCR amplicons indicated that the A. gerardii rhizospheres host phylogenetically diverse fungal communities and that these communities are seasonally dynamic. Operational taxonomic units with Basic Local Alignment Search Tool affinities within the order Helotiales were dominant in the rhizosphere in May. These putative saprobes were largely replaced by arbuscular mycorrhizal fungi with likely affinities within Glomerales suggesting that the fungal communities are not only compositionally but also functionally dynamic. These data suggest replacement of functional guilds comprised of saprobic fungi by mutualistic fungi in the course of a growing season.

10aRhizosphere10aRibosomal RNA10aSeasonal dynamics10atallgrass prairie1 aJumpponen, A. uhttps://link.springer.com/article/10.1007%2Fs00572-010-0358-702332nas a2200193 4500008004100000245012700041210006900168300001300237490000700250520168600257100001901943700001701962700001801979700001401997700001402011700001702025700001902042856007702061 2011 eng d00aSpecies abundance distributions and richness estimations in fungal metagenomics – lessons learned from community ecology0 aSpecies abundance distributions and richness estimations in fung a275 -2850 v203 a

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities – phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data – a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.

1 aUnterseher, M.1 aDorman, C.F.1 aJumpponen, A.1 aMoora, M.1 aÖpik, M.1 aTedersoo, L.1 aSchnittler, M. uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2010.04948.x02385nas a2200205 4500008004100000245012100041210006900162300001300231490000800244520163800252653003401890653001201924653001701936653002701953653001801980100001801998700001702016700001802033856012802051 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://knz.lternet.edu/content/isolation-and-morphological-and-metabolic-characterization-common-endophytes-annually-burned01595nas a2200157 4500008004100000245014500041210006900186300001100255490000700266520097300273100001801246700001601264700001701280700001401297856012601311 2010 eng d00aMassively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites0 aMassively parallel 454sequencing of fungal communities in Quercu a41 -530 v193 aWe analysed two sites within and outside an urban development in a rural background to estimate the fungal richness, diversity and community composition in Quercus spp. ectomycorrhizas using massively parallel 454-sequencing in combination with DNA-tagging. Our analyses indicated that shallow sequencing (∼150 sequences) of a large number of samples (192 in total) provided data that allowed identification of seasonal trends within the fungal communities: putative root-associated antagonists and saprobes that were abundant early in the growing season were replaced by common ectomycorrhizal fungi in the course of the growing season. Ordination analyses identified a number of factors that were correlated with the observed communities including host species as well as soil organic matter, nutrient and heavy metal enrichment. Overall, our application of the high throughput 454 sequencing provided an expedient means for characterization of fungal communities.1 aJumpponen, A.1 aJones, K.L.1 aMattox, J.D.1 aYeage, C. uhttp://knz.lternet.edu/content/massively-parallel-454-sequencing-fungal-communities-quercus-spp-ectomycorrhizas-indicates01393nas a2200169 4500008004100000245015200041210006900193300001500262490000600277520073300283100001801016700001601034700001801050700001601068700001701084856012201101 2010 eng d00aMulti-element fingerprinting and high throughput sequencing identify multiple elements that affect fungal communities in Quercus macrocarpa foliage0 aMultielement fingerprinting and high throughput sequencing ident a1157 -11610 v53 aDiverse fungal mutualists, pathogens and saprobes colonize plant leaves. These fungi face a complex environment, in which stochastic dispersal interplays with abiotic and biotic filters. However, identification of the specific factors that drive the community assembly seems unattainable. We mined two broad data sets and identified chemical elements, to which dominant molecular operational taxonomic units (OTUs) in the foliage of a native tree respond most extremely. While many associations could be identified, potential complicating issues emerged. Those were related to unevenly distributed OTU frequency data, a large number of potentially explanatory variables, and the disproportionate effects of outlier observations.1 aJumpponen, A.1 aKeating, K.1 aGadbury, G.L.1 aJones, K.L.1 aMattox, J.D. uhttp://knz.lternet.edu/content/multi-element-fingerprinting-and-high-throughput-sequencing-identify-multiple-elements02016nas a2200133 4500008004100000245012200041210006900163300001300232490000800245520151300253100001801766700001601784856008201800 2010 eng d00aSeasonally dynamic fungal communities in Quercus macrocarpa phyllosphere differ among urban and nonurban environments0 aSeasonally dynamic fungal communities in Quercus macrocarpa phyl a496 -5130 v1863 a

•The fungal richness, diversity and community composition in the Quercus macrocarpa phyllosphere were compared across a growing season in trees located in six stands within and outside a small urban center using 454-sequencing and DNA tagging. The approaches did not differentiate between endophytic and epiphytic fungal communities. •Fungi accumulated in the phyllosphere rapidly and communities were temporally dynamic, with more than a third of the analyzed operational taxonomic units (OTUs) and half of the BLAST-inferred genera showing distinct seasonal patterns. The seasonal patterns could be explained by fungal life cycles or environmental tolerances. •The communities were hyperdiverse and differed between the urban and nonurban stands, albeit not consistently across the growing season. Foliar macronutrients (nitrogen (N), potassium (K) and sulfur (S)), micronutrients (boron (B), manganese (Mn) and selenium (Se)) and trace elements (cadmium (Cd), lead (Pb) and zinc (Zn)) were enriched in the urban trees, probably as a result of anthropogenic activities. Because of correlations with the experimental layout, these chemical elements should not be considered as community drivers without further empirical studies. •We suggest that a combination of mechanisms leads to differences between urban and nonurban communities. Among those are stand isolation and size, nutrient and pollutant accumulation plus stand management, including fertilization and litter removal.

1 aJumpponen, A.1 aJones, K.L. uhttps://nph.onlinelibrary.wiley.com/doi/full/10.1111/j.1469-8137.2010.03197.x02495nas a2200205 4500008004100000245007400041210006900115300001500184490000800199520186400207653001902071653001902090653001502109653001502124653002202139100001802161700001602179700002002195856007402215 2010 eng d00aVertical distribution of fungal communities in tallgrass prairie soil0 aVertical distribution of fungal communities in tallgrass prairie a1027 -10410 v1023 a

We used 454 sequencing of the internal transcribed spacer region to characterize fungal communities in tallgrass prairie soils subdivided into strata 0–10, 10–20, 30–40 and 50–60 cm deep. The dataset included more than 14 000 fungal sequences distributed across Basidiomycota, Ascomycota, basal fungal lineages and Glomeromycota in order of decreasing frequency. As expected the community richness and diversity estimators tended to decrease with increasing depth. Although species richness was significantly reduced for samples from the deeper profiles, even the deepest stratum sampled contained richness of more than a third of that in the topmost stratum. More importantly, nonparametric multidimensional scaling (NMS) ordination analyses indicated that the fungal communities differed across vertical profiles, although only the topmost and deepest strata were significantly different when the NMS axis scores were compared by ANOVA. These results emphasize the importance of considering the fungal communities across the vertical strata because the deeper soil horizons might maintain a distinct community composition and thus contribute greatly to overall richness. The majority of operational taxonomic units (OTUs) declined in frequency with increasing depth, although a linear regression analysis indicated that some increased with increasing depth. The OTUs and BLAST-assigned taxa that showed increasing frequencies were mainly unculturable fungi, but some showed likely affinities to families Nectriaceae and Venturiaceae or to genus Pachnocybe. Although the ecological roles of the fungi in the deeper strata remain uncertain, we hypothesize that the fungi with preferences for deeper soil have adequate access to substrates and possess environmental tolerances that enable their persistence in those environments.

10a454 sequencing10apyrosequencing10asoil depth10aSoil fungi10atallgrass prairie1 aJumpponen, A.1 aJones, K.L.1 aBlair, John, M. uhttps://www.tandfonline.com/doi/abs/10.3852/09-316?journalCode=umyc2001384nas a2200145 4500008004100000245006700041210006700108260002800175300001100203520090600214100001801120700001401138700001901152856006701171 2009 eng d00aAnalysis of rhizosphere fungal communities using rRNA and rDNA0 aAnalysis of rhizosphere fungal communities using rRNA and rDNA bSpringer-Verlag, Berlin a29 -403 aMicrobial communities in soil and rhizosphere are diverse. Use of sequence data derived from environmental samples has become somewhat of a standard to explore the microbial diversity and community composition in soils. While the DNA encoding the ribosomal RNA genes can be easily PCR-amplified from many environmental samples, this DNA may carry a historical fingerprint, as naked DNA or as dormant, but inactive organisms. The use of ribosomal RNA may provide a tool to focus on the active organisms. This chapter describes kit-based methods to simultaneously extract DNA and RNA from environmental samples, and outlines a protocol for reverse-transcribing ribosomal RNA for PCR amplification of the produced cDNA. The fungal communities observed via sequencing the ribosomal RNA or the ribosomal RNA encoding DNA from Andropogon gerardii rhizosphere are compared, and the results briefly discussed.1 aJumpponen, A.1 aVarma, A.1 aKharkwal, A.C. uhttp://link.springer.com/chapter/10.1007%2F978-3-540-95894-9_201764nas a2200133 4500008004100000245015500041210006900196300001300265490000800278520122800286100001801514700001601532856008201548 2009 eng d00aMassively parallel 454-sequencing of Quercus macrocarpa phyllosphere fungal communities indicates reduced richness and diversity in urban environments0 aMassively parallel 454sequencing of Quercus macrocarpa phyllosph a438 -4480 v1843 a

• This study targeted the fungal communities in the phyllosphere of Quercus macrocarpa and compared the fungal species richness, diversity and community composition among trees located within and outside a small urban center using recently developed 454 sequencing and DNA tagging. • The results indicate that the fungal phyllosphere communities are extremely diverse and strongly dominated by ascomycetes, with Microsphaeropsis [two Operational Taxonomic Units (OTUs); 23.6%], Alternaria (six OTUs; 16.1%), Epicoccum (one OTU; 6.0%) and Erysiphe (two OTUs; 5.9%) as the most abundant genera. • Although the sequencing effort averaged 1000 reads per tree and detected nearly 700 distinct molecular OTUs at 95% internal transcribed spacer 1 similarity, the richness of the hyperdiverse phyllosphere communities could not be reliably estimated as nearly one-half of the molecular OTUs were singletons. • The fungal communities within and outside the urban center differed in richness and diversity, which were lower within the urban development. The two land-use types contained communities that were distinct and more than 10% of the molecular OTUs differed in their frequency.

1 aJumpponen, A.1 aJones, K.L. uhttps://nph.onlinelibrary.wiley.com/doi/full/10.1111/j.1469-8137.2009.02990.x00557nas a2200145 4500008004100000245008500041210006900126260002800195300001100223100001900234700001800253700001800271700001400289856010800303 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://knz.lternet.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%2Fs00572-008-0165-602816nas a2200193 4500008004100000245009000041210006900131300001300200490000700213520214500220653001402365653003402379653003002413653001402443653001502457100001802472700001802490856011402508 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://knz.lternet.edu/content/abundance-and-possible-functions-root-colonising-dark-septate-endophytic-fungi02158nas a2200205 4500008004100000245015200041210006900193300001500262490000700277520141300284653001701697653002501714653001001739653001301749653001801762653001301780100001801793700001801811856012301829 2005 eng d00aCan rDNA analyses of diverse fungal communities in soil and rootsdetect effects of environmental manipulations--a case study from tallgrass prairie0 aCan rDNA analyses of diverse fungal communities in soil and root a1177 -11940 v973 a

We tested whether fungal communities are impacted by nitrogen deposition or increased precipitation by PCR-amplifying partial fungal rRNA genes from 24 soil and 24 root samples from a nitrogen enrichment and irrigation experiment in a tallgrass prairie at Konza Prairie Biological Station in northeastern Kansas, U.S.A. Obtained fungal sequences represented great fungal diversity that was distributed mainly in ascomycetes and basiodiomycetes; only a few zygomycetes and glomeromycetes were detected. Conservative extrapolated estimates of the fungal species richness suggest that the true richness may be at least twice as high as observed. The effects of nitrogen enrichment or irrigation on fungal community composition, diversity or clone richness could not be unambiguously assessed because of the overwhelming diversity. However, soil communities differed from root communities in diversity, richness and composition. The compositional differences were largely attributable to an abundant, soil-inhabiting group placed as a well-supported sister group to other ascomycetes. This group likely represents a novel group of fungi. We conclude that the great fungal richness in this ecosystem precluded a reliable assessment of anthropogenic impacts on soil or rhizosphere communities using the applied sampling scheme, and that detection of novel fungi in soil may be more a rule than an exception.

10aBiodiversity10aenvironmental change10afungi10anitrogen10aPrecipitation10asoil DNA1 aJumpponen, A.1 aJohnson, L.C. uhttp://knz.lternet.edu/content/can-rdna-analyses-diverse-fungal-communities-soil-and-rootsdetect-effects-environmental01757nas a2200205 4500008004100000245014500041210006900186300001300255490000700268520099200275653002601267653002401293653001801317653002201335100001801357700001901375700001801394700001801412856012101430 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://knz.lternet.edu/content/nitrogen-enrichment-causes-minimal-changes-arbuscular-mycorrhizal-colonization-shifts