ISI peer-reviewed

  • Wilhelm RC, Cardenas E, Leung H, Maas K, Hartmann M, Hahn A, Hallam S et al. (2017). A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting. Scientific Data 4: 170092.
  • Degrune F, Theodorakopoulos N, Colinet G, Hiel MP, Bodson B, Taminiau B, Daube G, Vandenbol M, Hartmann M (2017). Temporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes. Frontiers in Microbiology 8: 1127.
  • Moll J, Klingenfuss F, Widmer F, Gogos A, Bucheli TD, Hartmann M*, van der Heijden MGA (2017). Effects of titanium dioxide nanoparticles on soil microbial communities and wheat biomass. Soil Biology & Biochemistry 111: 85-93. * joint last author
  • Hartmann M, Brunner I, Hagedorn F, Bardgett RD, Stierli B, Herzog C, Chen X, Zingg A, Graf-Pannatier E, Rigling A, Frey B (2017). A decade of irrigation transforms the soil microbiome of a semi-arid pine forest. Molecular Ecology 26: 1190-1206.
  • Frossard A, Hartmann M, Frey B (2017). Tolerance of the forest soil microbiome to increasing mercury concentrations. Soil Biology & Biochemistry 105:162-176.
  • Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, Hartmann M (2016). Microbial diversity in European alpine permafrost and active layers. FEMS Microbiology Ecology (doi:10.1093/femsec/fiw018).
  • Rime T, Hartmann M, Frey B (2016). Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. The ISME Journal 10: 1625-1641.
  • Rime T, Hartmann M, Stierli B, Anesio AM, Frey B (2016). Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields. Soil Biology & Biochemistry 98: 30-41.
  • Deslippe JR, Hartmann M, Grayston SJ, Simard SW, Mohn WW (2016). Stable isotope probing implicates a species of Cortinarius in carbon transfer through ectomycorrhizal fungal mycelial networks in Arctic tundra. New Phytologist 210: 383-390.
  • van der Heijden MGA, Hartmann M (2016). Networking in the Plant Microbiome. PLOS Biology 14: e1002378.
  • Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, Beman JM, Abell G, Philippot L, Prosser J, Foulquier A, Yuste JC, Glanville HC, Jones D, Angel R, Salminen J, Newton RJ, Bürgmann H, Ingram LJ, Hamer U, Siljanen HMP, Peltoniemi K, Potthast K, Bañeras L, Hartmann M, Banerjee S, Yu RQ, Nogaro G, Richter A, Koranda M, Castle S, Goberna M, Song B, Chatterjee A, Nunes OC, Lopes AR, Cao Y, Kaisermann A, Hallin S, Strickland MS, Garcia-Pausas J, Barba J, Kang H, Isobe K, Papaspyrou S, Pastorelli R, Lagomarsino A, Lindström E, Basiliko N, Nemergut DR (2016). Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Frontiers in Microbiology 7: 214.
  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH (2015). Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources 15: 1403-1414.
  • Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson KH, Kõljalg U, Edgar RC, Abarenkov K (2015). A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes & Environment: 30: 145-150.
  • Hartmann M, Frey B, Mayer J, Mäder P, Widmer F (2015). Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal 9: 1177-1194.
  • Rime T, Hartmann M, Brunner I, Widmer F, Zeyer J, Frey B (2015). Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. Molecular Ecology 24: 1091-1108.
  • Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, Lüscher P, Widmer F, Frey B (2014). Resistance and resilience of the forest soil microbiome to logging-associated compaction. The ISME Journal 8: 226-244.
  • Nilsson RH, Hyde KD, Pawłowska J, Ryberg M, Tedersoo L, Bjørnsgard Aas A, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Guldberg Frøslev T, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl BD, Lindner D, Liu JK, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Liparini Pereira O, Batista Pinho D, Porter TM, Queloz V, Riit T, Sánchez-García M, de Sousa F, Stefańczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson KH, Kõljalg U, Abarenkov K (2014). Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity 67: 11-19.
  • Kõljalg U, Nilsson HR, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiß M, Larsson KH (2013). Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology 22: 5271–5277.
  • Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, De Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH (2013). Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution 4: 914-919.
  • Kerekes J, Kaspari M, Stevenson B, Nilsson RH, Hartmann M, Amend A, Bruns TD (2013). Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest. Molecular Ecology 22: 2827-2838.
  • Hyde KD, Udayanga D, Manamgoda DS, Tedersoo L, Larsson E, Abarenkov K, Bertrand YJK, Oxelman B, Hartmann M, Kauserud H, Ryberg M, Kristiansson E, Nilsson HR (2013). Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Current Research in Environmental & Applied Mycology 3: 1-32.
  • VanInsberghe D, Hartmann M, Stewart GR, Mohn WW (2013). Isolation of a substantial proportion of bacterial forest soil communities as detected via pyrotag sequencing. Applied and Environmental Microbiology 79: 2096-2098.
  • Dimitriu PA, Boyce G, Samarakoon A, Hartmann M, Johnson P, Mohn WW (2013). Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity. Environmental Microbiology Reports 5: 200-210.
  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH (2013). Metaxa, overview. In:Nelson K. (Ed.) Encyclopedia of Metagenomics. Springer Reference, Springer-Verlag Berlin Heidelberg.
  • Hartmann M, Howes CG, VanInsberghe D, Yu H, Bachar D, Christen R, Nilsson RH, Hallam SJ, Mohn WW (2012). Significant and persistent impact of timber Harvesting on soil microbial communities in Northern coniferous forests. The ISME Journal 6: 2199-2218.
  • Gill N, Ferreira RBR, Antunes LCM, Willing BP, Sekirov I, Al-Zahrani F, Hartmann M, Finlay BB (2012). Neutrophil elastase alters the murine gut microbiota resulting in enhanced Salmonella colonization. PLoS ONE 7: e49646.
  • Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson J, Eriksson M, Larsson KH, Larsson E, Kõljalg U (2012). Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-63.
  • Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH (2012). Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Research in Microbiology 163: 407-412.
  • Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L, Wlodarska M, Gill N, Blanchet M-R, Mohn WW, McNagny KM, Finlay BB (2012). Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Reports 13: 440-447.
  • Deslippe JR, Hartmann M, Simard SW, Mohn WW (2012). Long-term warming alters the composition of Arctic soil microbial communities. FEMS Microbiology Ecology 82(2): 303-315.
  • Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH (2011). Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (SSU/12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek 100(3): 471-475.
  • Nilsson RH, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Betrand Y, Alfredsson JF, Larsson KH, Kõljalg, U, Abarenkov K (2011). A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation. Mycoscience 52(4): 278-282.
  • Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Hallam SJ, Mohn WW, Nilsson RH (2011). V-RevComp: Automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiology Letters 319(2): 140-145.
  • Deslippe JR, Hartmann M, Mohn WW, Simard SW (2011). Long-term experimental manipulation of climate alters the ectomycorrhizal community of Betula nana in Arctic tundra. Global Change Biology 17(4): 1625-1636.
  • Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH (2010). V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. Journal of Microbiological Methods 83(2): 250-253.
  • Nilsson RH, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J, Kristiansson E, Ryberg M, Jumpponen A, Abarenkov K (2010). An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecology 3(4): 284-287.
  • Schneider S, Hartmann M, Enkerli J, Widmer F (2010). Fungal community structure in soils of conventional and organic farming systems. Fungal Ecology 3(3): 215-224.
  • Hartmann M, Lee S, Hallam SJ, Mohn WW (2009). Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Environmental Microbiology 11(12): 3045-3062.
  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009). Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75(23): 7537-7541.
  • Hartmann M, Widmer F (2008). Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling. FEMS Microbiology Ecology 63(2): 249-260.
  • Hartmann M, Enkerli J, Widmer F (2007). Residual polymerase activity induced bias in terminal restriction fragment length polymorphism analysis. Environmental Microbiology 9(2): 555-559.
  • Hartmann M, Widmer F (2006). Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Applied and Environmental Microbiology 72(12): 7804-7812.
  • Lazzaro A, Hartmann M, Blaser P, Widmer F, Schulin R, Frey B (2006). Bacterial community structure and activity in different Cd-treated forest soils. FEMS Microbiology Ecology 58(2): 278-292.
  • Hartmann M, Fliessbach A, Oberholzer H-R, Widmer F (2006). Ranking the magnitude of crop and farming system effects on soil microbial biomass and genetic structure of bacterial communities. FEMS Microbiology Ecology 57(3): 378-388.
  • Oberholzer H-R, Wysser M, Hartmann M, Widmer F (2006). Regeneration of impaired biological soil properties caused by physical soil impact. In: Soil management for Sustainability. Advances in GeoEcology (Horn R, Fleige H, Peth S, Peng X, Eds.). pp. 140-148. Catena Verlag, Reiskirchen, Germany.
  • Widmer F, Rasche F, Hartmann M, Fliessbach A (2006). Community structures and substrate utilization of bacteria in soils from organic and conventional farming systems of the DOK long-term field experiment. Applied Soil Ecology 33(3): 294-307.
  • Widmer F, Hartmann M, Frey B, Koelliker R (2006). A novel strategy to extract specific phylogenetic sequence information from community T-RFLP. Journal of Microbiological Methods 66(3): 512-520.
  • Hartmann M, Frey B, Koelliker R, Widmer F (2005). Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches. Journal of Microbiological Methods 61(3): 349-360.

Public Outreach

  • Hartmann M, Frey B (2015). Mikrobiom-Forschung an der WSL. Natur und Landschaft Inside 4: 18-23.
  • Frey B, Widmer F, Hartmann M (2015). Grossflächige Untersuchungen der Bodenbiodiversität sind endlich realisierbar? Hotspot - Biodiversität im Boden 32: 16-17.
  • Fliessbach A, Mäder P, Mayer J, Oehl F, Pfiffner L, Hartmann M, Widmer F (2015). Welche landwirtschaftlichen Anbausysteme fördern das Bodenleben? Hotspot - Biodiversität im Boden 32: 8-9.
  • Frey B, Hartmann M (2013) Biodiversität von Waldböden – Auswirkungen des Einsatzes von Holzerntemaschinen auf mikrobielle Gemeinschaften. Forum für Wissen 2013 - Bodenschutz im Wald: 61-69.
  • Hartmann M, Kölliker R, Widmer F (2006). Populationsstrukturen von Bodenbakterien in verschiedenen Anbausystemen. Bulletin SGPW/SSA 20: 15.
  • Hartmann M, Fliessbach A, Kölliker R, Enkerli J, Dubois D, Widmer F (2006). Anbausysteme beeinflussen Bodenbakterien. Agrarforschung 13: 494-499.
  • Hartmann M, Widmer F (2005). Der Boden lebt! - Der Vielfalt von Mikroorganismen auf der Spur. Hotspot 11: 18.


Conference Contributions

  • Member of International Scientific Committee - 3rd Thünen Symposium on Soil Metagenomics (SM2016), 14-16 Dec 2016, Braunschweig, Germany.
  • Convenor of Roundtable - Hartmann M, Jia Z, Tiedje J. Soil metagenomics - deciphering big data. 16th International Symposium on Microbial Ecology, 21-26 Aug 2016, Montreal, Canada.


Invited Presentations

  • Hartmann M (2017) A decade of irrigation transforms the soil microbiome of a semi-arid pine forest. Biology Seminar Series, Swiss Federal Research Institute WSL, March 29, Birmensdorf, Switzerland.
  • Hartmann M (2017). A decade of irrigation transforms the soil microbiome of a water-limited pine forest. Biology Seminar Series at the University of Neuchâtel, March 23, Neuchâtel, Switzerland.
  • Hartmann M (2016) Climate change transforms the forest soil microbiome and associated ecosystem processes. 3rd Thünen Symposium on Soil Metagenomics, December 14-16, Braunschweig, Germany.
  • Hartmann M (2016). The alpine cryosphere microbiome in the face of climate change. Geo-Bio Seminar Series at the German Research Center for Geosciences GFZ, October 11, Potsdam, Germany.
  • Hartmann M (2015) Soil microbial communities as sentinels of environmental change. 7th Annual Soil Metagenomics Meeting, October 21-23, Hilton Lisle/Naperville, Naperville, USA.
  • Hartmann M (2014) Microbial ecology in the sequencing era. Research School in “Infection, Inflammation and Immunity”, June 2-13, University of Tromsø, Tromsø, Norway.
  • Hartmann M (2014) Deep targeted sequencing to study the microbiome in clinical and natural systems. Research School in “Infection, Inflammation and Immunity”, June 2-13, University of Tromsø, Tromsø, Norway.
  • Hartmann M (2014) Deep targeted sequencing to explore the microbiome in clinical and environmental systems. May 9, University of Helsinki, Helsinki, Finnland.


Conference Presentations (Oral)

  • Hartmann M, Brunner, I, Hagedorn F, Rigling A, Frey B (2015). A decade of irrigation transforms the soil microbiome of a semi-arid pine forest. Ecology of Soil Microorganisms 2015, November 29 - December 3, Prague, Czech Republic.
  • Hartmann M, Rime T, Hajdas I, Phillips M, Frey B (2015) Unraveling the unknown microbial diversity hidden in alpine permafrost. 6th International Conference of Polar and Alpine Microbiology - PAM2015, September 6-9, České Budějovice, Czech Republic.
  • Hartmann M, Widmer F (2014) The response of soil microbial diversity to long-term organic and conventional farming. Zurich Mycology Symposium, January 24, Zurich, Switzerland.
  • Hartmann M, Schneider S, Frey B, Widmer F (2013) The response of soil microbial diversity to long-term organic and conventional farming. 2nd Thünen Symposium on Soil Metagenomics, December 11-13, Braunschweig, Germany.
  • Hartmann M, Schmutz S, Widmer F, Frey B (2013) Soil compaction caused by logging operations persistently alters microbial diversity, structure and function. 5th Swiss Microbial Ecology (SME) Meeting, February 4-6, Murten, Switzerland.
  • Hartmann M (2013) Soil compaction caused by logging operations persistently alters fungal diversity and community structure as assessed by massively parallel pyrosequencing. Zurich Mycology Symposium, January 25, Zurich, Switzerland.
  • Hartmann M, Hallam S, Mohn W (2012) Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests. 14th International Symposium on Microbial Ecology (ISME 14), August 19-25, Copenhagen, Denmark.
  • Hartmann M (2011) Soil microbial communities as sentinels for environmental change associated with forest management. UBC Microbiology & Immunology Symposium, May 27, Vancouver BC, Canada.
  • Hartmann M (2011) Soil microbial communities as sentinels for environmental change associated with forest management. Annual Conference of the Centre for Microbial Diversity and Evolution (CMDE 2011), May 11-13, Harrison Hot Springs, Canada.
  • Hartmann M, Yu H, Howes CG, Hallam SJ, Mohn WW (2010). Effects of soil compaction and organic matter removal on forest soil bacterial and fungal communities. 13th International Symposium on Microbial Ecology (ISME 13), August 22-27, Seattle, USA.
  • Hartmann M, Hallam SJ, Mohn WW (2009). Long-term effects of timber management on bacterial, archaeal and eukaryal communities in northern coniferous forests of British Columbia. BAGECO 10, June 15-19, Uppsala, Sweden.
  • Hartmann M, Lee S, Chapman WK, Hallam SJ, Mohn WW (2008). Changes of microbial indicators along a soil depth profile in harvested forests. UBC Microbiology & Immunology Symposium, October 24, Vancouver BC, Canada.
  • Hartmann M, Lee S, Hallam SJ, Mohn WW (2008). Long-term effects of timber harvesting on soil microbial community structures at the 3-domain level. Centre for Microbial Diversity and Evolution (CMDE) – Annual Retreat 2008, May 28-30, Rockwater Secret Cove BC, Canada.
  • Hartmann M, Lee S, Chapman WK, Hallam SJ, Mohn WW (2008). Long-term effects of timber harvesting on soil microbial community structures along a depth gradient. Canadian Society of Soil Science (CSSS) 2008, July 6-10, Prince George BC, Canada.
  • Hartmann M, Widmer F (2007). Do genetic profiles reliably reflect changes in microbial community structures? BAGECO 9, June 23-27, Wernigerode, Germany.
  • Hartmann M, Widmer F (2006). Is soil bacterial diversity reflecting changes in agricultural productivity? Second Swiss Microbial Ecology Meeting, September 28-29, Bellinzona, Switzerland.
  • Hartmann M, Kölliker, R, Widmer F (2006). Populationsstrukturen von Boden-Bakterien in verschiedenen Anbausystemen. Tagung der Schweizerischen Gesellschaft für Pflanzenbauwissenschaften (SGPW), March 24, Bern, Switzerland.
  • Hartmann M, Widmer F (2004). Comparison of soil bacterial community structures in different agricultural management systems as determined with T-RFLP and RISA. First Swiss Microbial Ecology Meeting, September 23-24, Neuenburg, Switzerland.
  • Hartmann M, Frey B, Kölliker R, Widmer F (2004). Semi-automated genetic analyses of soil microbial communities: a comparison of T-RFLP and RISA. Annual Meeting of the VAAM. March 28-31, Braunschweig, Germany.