ENVIRONMENTAL MICROBIOLOGY Distinct Communities of Poplar Endophytes on an Unpolluted and a Risk Element-Polluted Site and Their Plant Growth-Promoting Potential In Vitro C. S. Schmidt 1 & P. Lovecká 2 & L. Mrnka 1 & A. Vychodilová 2 & M. Strejček 2 & M. Fenclová 2 & K. Demnerová 2 Received: 21 June 2017 /Accepted: 9 October 2017 # Springer Science+Business Media, LLC, part of Springer Nature 2017 Abstract Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts’ fitness both in nutrient-limited and pol- luted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests. Bacterial communities at the unpolluted site were dominated by Gammaproteobacteria with Pseudomonas sp. as the prominent member of the class, followed by Bacilli with prevailing Bacillus sp., whereas Alphaproteobacteria, mostly Rhizobium sp., prevailed at the polluted site. The fungal endophytic community was domi- nated by Ascomycetes and highly distinct on both sites. Dothideomycetes, mostly Cladosporium, prevailed at the non-polluted site while unclassified Sordariomycetous fungi dominated at the polluted site. Species diversity of endophytes was higher at the unpolluted site. Many tested endophytic strains solubilized phosphate and produced siderophores, phy- tohormones, and antioxidants. Some strains also exhibited ACC-deaminase activity. Selected bacteria showed high toler- ance and the ability to accumulate risk elements, making them promising candidates for use in inocula promoting biomass production and phytoremediation. Keywords Endophytes . PGPB . Sordariomycetes . Poplar . Risk elements . Phytoremediation Abbreviations AA Ascorbic acid ACC 1-Aminocyclopropane-1-carboxylate CAS Chrome azurol S DSE Dark septate endophytes DW Dry weight DPPH 2,2-Diphenyl-1-picrylhydrazyl HDTMA Hexadecyltrimethylammonium bromide IAA Indole-3-acetic acid iP N6-(Δ2-isopentenyl)adenine iPR N6-(Δ2-isopentenyl)adenosine LB Luria-Bertani broth MALDI-TOF MS Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry MEA Malt extract agar MIC Minimum inhibitory concentration PGP Plant growth promoting SNA Synthetic nutrient poor agar SD Standard deviation TSA Tryptic soy agar Highlights Communities of poplar endophytic bacteria and fungi were largely distinct on a risk elements-polluted and an unpolluted site. Rhizobia and a novel yet undescribed group of Sordariomycetous fungi dominated the risk elements-polluted site. Many poplar endophytes showed promising plant growth promoting and/or stress attenuating traits when studied in vitro. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00248-017-1103-y) contains supplementary material, which is available to authorized users. * C. S. Schmidt Christoph.Schmidt@ibot.cas.cz 1 Institute of Botany ASCR, Zámek 1, 252 43 Průhonice, Czech Republic 2 University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6, Czech Republic Microb Ecol https://doi.org/10.1007/s00248-017-1103-y