• Palmieri F, Magnin M, Diserens J, Gresse M, Bernasconi E, Pernot J, Shanmuganathan A, Trompette A, Von Garnier C, Junier T, Neuenschwander S, Bindschedler S, Pagni M, Koutsokera A, Ubags N, Junier P. One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus conidia. Preprints 2023, 2023052247. https://doi.org/10.20944/preprints202305.2247.v1
• Bernier LS, Estoppey A, Bindschedler S, Stan GB, Junier P, Stanley CE. Microfluidic platform for microbial spore germination studies in multiple growth conditions. BMC Methods 1, 12 (2024). https://doi.org/10.1186/s44330-024-00012-5
• Leins A, Bregnard D, Schäpan I, van Zonnevald W, Bindschedler S, Vieth-Hillebrand A, Junier P, Regenspurg S. In preparation for Geothmeral fluid properties at extreme conditions, Eds: Baba A, Milsch H, Regenspurg S. Assessment of the Pb(II) biosorption potential of the fungus Penicillium citrinum under geothermal conditions. GFZ Data Services. https://doi.org/10.5880/fidgeo.2024.006
• Junier G, Cailleau G, Fatton M, Udriet P, Hashmi I, Bregnard D, Corona-Ramirez A, de Francesco E, Kuhn T, Mangia N, Zhioua S, Hunkeler D, Bindschedler S, Sieber S, Gonzalez D. A cohesive Microcoleus strain cluster causes benthic cyanotoxic blooms in rivers worldwide. Water Research X 24, 100252
• Clark AJ, Masters-Clark E, Moratto E, Junier P, Stanley CE. Visualizing liquid distribution across hyphal networks with cellular resolution. Biomicrofluidics. 2024 Oct 7;18(5):054109. doi: 10.1063/5.0231656. PMID: 39381835; PMCID: PMC11460992.
• Kelliher JM, Johnson LYD, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PSG. Fabricated devices for performing bacterial-fungal interaction experiments across scales. Front Microbiol. 2024 Aug 7;15:1380199. doi: 10.3389/fmicb.2024.1380199. PMID: 39171270; PMCID: PMC11335632.
• Cailleau G, Junier T, Paul C, Fatton M, Corona-Ramirez A, Gning O, Beck K, Vidal J, Bürgmann H, Junier P. Temporal and spatial changes in the abundance of antibiotic resistance gene markers in a wastewater treatment plant. Water Environ Res. 2024 Aug;96(8):e11104. doi: 10.1002/wer.11104. PMID: 39164119.
• Cravero M, Ruelle J, Bindschedler S, Emler S, Junier P. Using a Centroid-based approach for a reliable identification of morels (Morchella spp.): A case study for food authentication. J Food Sci. 2024 Aug;89(8):4745-4757. doi: 10.1111/1750-3841.17219. Epub 2024 Jul 2. PMID: 38955792.
• Petrasz P , Zhioua S, James S, Bindschedler S, Junier P, Joseph E. Green Alternatives for Archaeological Iron Stabilization. 2024. Studies in Conservation, 69(sup1), 270–280. https://doi.org/10.1080/00393630.2024.2336880
• Regenspurg S, Blöcher G, Bregnard D, Hehn V, Huenges E, Junier P, Kieling K, Kluge C, Kranz S, Leins A, Vieth-Hillebrand A, Wiersberg T, Zimmer M. Geochemical and microbial processes in a deep geothermal well during seven years of production stop and their potential impact on the well performance. 2024. Geothermics, 120, 102979, ISSN 0375-6505, https://doi.org/10.1016/j.geothermics.2024.102979.
• Brandenburg L, Fatton M, Patty L, Grone J, Meyer E, Schroffenegger U, Bindschedler S, Junier P, Demory B-O. Homochiral Biosignatures: A Spectropolarimetric Approach to Microbial Life Detection 2024 Astrobiology Science ConferencePatty L, Grone J, Fatton M, Brandenburg L, Schroffenegger U, Meyer E, Junier P, Demory B-O. Remote detection of life through spectropolarimetry in the visible. 2024 Astrobiology Science Conference
• Grone J, Patty L, Brandenburg L, Fatton M, U Schroffenegger, Meyer E, Junier P, Demory B-O. Full-Stokes Spectropolarimetric Modelling of Potential Ocean-World Microbial Biosignatures. 2024 Astrobiology Science Conference
• Fatton M, Brandenburg L, Patty L, Grone J, Meyer E, S Bindschedler, U Schroffenegger, Junier P, Demory B-O. Investigating the Impact of Different Environmental Conditions on Photosynthetic Pigments of Cyanobacteria: Spectropolarimetry and Homochirality as a Proxy. 2024 Astrobiology Science Conference
• Timmis K, Hallsworth JE, McGenity TJ, Armstrong R, Colom MF, Karahan ZC, Chavarría M, Bernal P, Boyd ES, Ramos JL, Kaltenpoth M, Pruzzo C, Clarke G, López-Garcia P, Yakimov MM, Perlmutter J, Greening C, Eloe-Fadrosh E, Verstraete W, Nunes OC, Kotsyurbenko O, Nikel PI, Scavone P, Häggblom MM, Lavigne R, Le Roux F, Timmis JK, Parro V, Michán C, García JL, Casadevall A, Payne SM, Frey J, Koren O, Prosser JI, Lahti L, Lal R, Anand S, Sood U, Offre P, Bryce CC, Mswaka AY, Jores J, Kaçar B, Blank LM, Maaßen N, Pope PB, Banciu HL, Armitage J, Lee SY, Wang F, Makhalanyane TP, Gilbert JA, Wood TK, Vasiljevic B, Soberón M, Udaondo Z, Rojo F, Tamang JP, Giraud T, Ropars J, Ezeji T, Müller V, Danbara H, Averhoff B, Sessitsch A, Partida-Martínez LP, Huang W, Molin S, Junier P, Amils R, Wu XL, Ron E, Erten H, de Martinis ECP, Rapoport A, Öpik M, Pokatong WDR, Stairs C, Amoozegar MA, Serna JG. A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society. Microb Biotechnol. 2024 May;17(5):e14456. doi: 10.1111/1751-7915.14456. PMID: 38801001; PMCID: PMC11129164.
• Bregnard D, Gonzalez D, Di Francesco E, Mangia N, Regenspurg S, Junier P. Complete genome sequence of Thermaerobacter composti strain Ins1, a spore-forming filamentous bacterium isolated from a deep geothermal reservoir. Microbiol Resour Announc. 2024 Apr 11;13(4):e0005824. doi: 10.1128/mra.00058-24. Epub 2024 Mar 13. PMID: 38477458; PMCID: PMC11008173.
• Estoppey A, Tinguely C, Cravero M, Blandenier E, Brand L, Court J, Zaninetti M, Bindschedler S, Junier P. Gamification as a tool to teach key concepts in microbiology to bachelor-level students in biology: a case study using microbial interactions and soil functioning. Access Microbiol. 2024 Feb 6;6(2):000699.v3. doi: 10.1099/acmi.0.000699.v3. PMID: 38482366; PMCID: PMC10928398.
• Bregnard D, Cailleau G, van Zonneveld W, Regenspurg S, Bindschedler S, Junier P. Co-isolation of Penicillium citrinum and its cell-switching partner Meyerozyma guilliermondii from a geothermal power plant. bioRxiv, 2024.06. 19.599737
• Bregnard D, Leins A, Vieth-Hillebrand A, Junier P, Regenspurg S, van Zonneveld W, Stammeier J, Iannotta J, Günther K. Lead(II) biosorption experiments of the fungus Penicillium citrinum under geothermal conditions. 2024. GFZ Data Services. https://doi.org/10.5880/fidgeo.2024.006
• Périat C, Kuhn T, Buffi M, Corona-Ramirez A, Fatton M, Cailleau G, Chain PS, Stanley CE, Wick LY, Bindschedler S, Gonzalez D, Li Richter XY, Junier P. Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks. Microlife. 2024 Feb 20;5:uqae004. doi: 10.1093/femsml/uqae004. PMID: 38463165; PMCID: PMC10924533.
• Cravero M, Bonito G, Chain PS, Bindschedler S, Junier P. A new species of true morel from Switzerland: Morchella helvetica, sp. nov. Mycologia. 2024 Nov-Dec;116(6):1101-1109. doi: 10.1080/00275514.2024.2397932. Epub 2024 Oct 18. PMID: 39423308.
• Palmieri, F., Diserens, J., Gresse, M., Magnin, M., Helle, J., Salamin, B., Bisanti, L., Bernasconi, E., Pernot, J., Shanmuganathan, A., Trompette, A., von Garnier, C., Junier, T., Neuenschwander, S., Bindschedler, S., Pagni, M., Koutsokera, A., Ubags, N., & P. Junier. 2024. One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus Conidia. Microorganisms, 12(10), 2025. https://doi.org/10.3390/microorganisms12102025
  Instead of the pre-print.

• Cailleau G, Hanson BT, Cravero M, Zhioua S, Hilpish P, Ruiz C, Robinson AJ, Kelliher JM, Morales D, Gallegos-Graves V, Bonito G, Chain PSG, Bindschedler S, Junier P. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp. Front Fungal Biol. 2023 Dec 13;4:1285531. doi: 10.3389/ffunb.2023.1285531. PMID: 38155707; PMCID: PMC10753826.
• Estoppey A, Tinguely C, Cravero M, Blandenier E, Brand L, Court J, Zaninetti M, Bindschedler S, Junier P. Gamification as a tool to teach key concepts in microbiology to bachelor-level students in biology: a case study using microbial interactions and soil functioning. Access Microbiol. 2024 Feb 6;6(2):000699.v3. doi: 10.1099/acmi.0.000699.v3. PMID: 38482366; PMCID: PMC10928398.
• Cravero M, Bonito G, Robinson AJ., Chain PSG, Bindschedler S, Junier P. Biodiversity of Morchella in Switzerland: a study highlighting the diversity of native black morels and the discovery of five new phylogenetic lineages, 23 October 2023, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-3344089/v1]
• Bregnard D, Leins A, Cailleau G, Vieth-Hillebrand A, Eichinger F, Ianotta J., Hoffmann R, Uhde J, Bindschedler S, Regenspurg S, Junier P. Unveiling microbial diversity in deep geothermal fluids, from current knowledge and analogous environments. Geotherm Energy 11, 28 (2023). https://doi.org/10.1186/s40517-023-00269-z
• Leins A, Bregnard D, Vieth-Hillebrand A, Poetz S, Eichinger F, Cailleau G, Junier P, Regenspurg S. Methods to characterize type, relevance, and interactions of organic matter and microorganisms in fluids along the flow path of a geothermal facility.Biogeosciences Discussions 2023, 1-37
• Trompette A, Shanmuganathan A, Pernot J, Palmieri F, Bernasconi E, Von Garnier C, Stucki J, Hobi N, Junier P, Koutsokera A, Ubags N. Fighting aspergillosis using biocontrol bacteria. European Respiratory Journal 2023 62: PA2186; DOI: 10.1183/13993003.congress-2023.PA2186
• Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales D, Cailleau G, Junier P, Bonito G, Chain PSG.The untapped potential of mini-microbiomes: challenges of endohyphal microbiomes. https://doi.org/10.21203/rs.3.rs-3311638/v1
• Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales D, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. Microbiome 11, 192 (2023). https://doi.org/10.1186/s40168-023-01634-7
• Kuhn T, Junier P, Bshary R, Terrettaz C, Gonzalez D, Richter XL. Nutrients and flow shape the cyclic dominance games between Escherichia coli strains. Philos Trans R Soc Lond B Biol Sci. 2023 May 8;378(1876):20210503. doi: 10.1098/rstb.2021.0503. Epub 2023 Mar 20. PMID: 36934746; PMCID: PMC10024984.
• Corona Ramirez A, Bregnard D, Junier T, Cailleau G, Dorador C, Bindschedler S, Junier P. Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis. BMC Microbiol. 2023 Mar 14;23(1):68. doi: 10.1186/s12866-023-02809-w. PMID: 36918804; PMCID: PMC10015814.
• Corona Ramírez A, Lee KS, Odriozola A, Kaminek M, Stocker R, Zuber B, Junier P. Multiple roads lead to Rome: unique morphology and chemistry of endospores, exospores, myxospores, cysts and akinetes in bacteria. Microbiology (Reading). 2023 Feb;169(2):001299. doi: 10.1099/mic.0.001299. PMID: 36804869; PMCID: PMC10197873.
• Buffi M, Cailleau G, Kuhn T, Li Richter XY, Stanley CE, Wick LY, Chain PS, Bindschedler S, Junier P. Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth. Microlife. 2023 Oct 18;4:uqad042. doi: 10.1093/femsml/uqad042. PMID: 37965130; PMCID: PMC10642649.
• Bregnard D, Leins A, Vieth-Hillebrand A, Regenspurg S, Junier P. The H2020 REFLECT project: Deliverable Deliverable_2.5 – Database of microbes and organic compounds, GFZ German Research Centre , DOI: https://doi.org/10.48440/gfz.4.8.2023.005
• Bindschedler S, Hilpisch P, Schmid E, Bregnard D, Alawi M, Regenspurg S, Junier P. Biomining of critical raw materials using the oxalate-carbonate pathway. Goldschmidt 2023 Conference

• Leins A, Bregnard D, Vieth‑Hillebrand A, Junier P Regenspurg S. 2022. Dissolved organic compounds in geothermal fluids used for energy production: a review. Geothermal Energy, 10:9 https://doi.org/10.1186/s40517-022-00220-8
• Junier, T., Paul, C., Corona-Ramirez, A., Filippidou, S., Fatton, M., Lehmann, A., Chain, P.S., Ariztegui, D., Vennemann, T., Viollier, P.H. & P. Junier. 2022. High diversity of lysis-resistant cells upon the application of targeted physical and chemical lysis to environmental samples originating from three different water bodies. Environmental DNA journal. Edn3.309.
• Corona-Ramirez, A., Cailleau, G., Fatton, M., Dorador, C. & P. Junier. 2022. Diversity of Lysis-resistant bacteria and archaea in the polyextreme environment of Salar de Huasco. Frontiers in Microbiology. 13: 826117.
• Dreier, M., Meola, M., Berthoud, H., Shani, N., Wechsler, D. & P. Junier. 2022. High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota. BMC Microbiology.22: 48.
• Estoppey, A., Weisskopf, L., Di Francesco, E., Vallat-Michel, A., Bindschedler, S., P.S. Chain & P. Junier. 2022. Improved methods to assess the effect of bacteria on germination of fungal spores. FEMS Microbiology Letters. 369(1): fnac034.
• Sebag, D., Verrecchia, E.P., Adatte, T., Aubert, M., Cailleau, G., Decaëns, T., Kowalewski, I., Trap, J., Bureau, F., Hedde, M.. 2022. Size fractions of organic matter pools influence their stability: Application of the Rock-Eval® analysis to beech forest soils. Pedosphere, 32;4, 565-575. https://doi.org/10.1016/S1002-0160(21)60050-4.
• Kuhn T, Buffi M, Bindschedler S, Chain PS, Gonzalez D, Stanley CE, Wick LY, Junier P, Richter XL. Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces. BMC Biol. 2022 Sep 14;20(1):203. doi: 10.1186/s12915-022-01406-z. PMID: 36104696; PMCID: PMC9476585.

• Robinson, A.J., House, G.L., Morales, D.P., Kelliher, J.M., Gallegos-Graves, L.V., LeBrun, E.S., Davenport, K.W., Palmieri, F., Lohberger, A., Bregnard, D., Estoppey, A., Buffi, M., Paul, C., Junier, T., Hervé, V., Cailleau, G., Lupini, S., Nguyen, H., Zheng, A.O., Jandelli-Gimenes, L., Bindschedller, S., Rodrigues, D.F., Werner, J.H. Young, J.D., Junier, P. & P.S. Chain. 2021. Widespread bacterial diversity within the bacteriome of fungi. Communications Biology ;4(1):1168.
• Domeignoz-Horta, L.A., Shinfuku, M., Junier, P., Poirier, S., Verrecchia, E., Sebag, D. & K.M. DeAngelis. 2021. Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence. ISME communication. 64.
• Fatton, M., Schneiter, A., Allisiardi, M., Hänni, L., Hauser, G., Gonçalves-Fernandes, Y., Pessina, A., Pijnenburg, M.L., Vaudroz, C., Bshary, A., S. Bindschedler*, P. Junier*. 2021. Microbes go to school: using microbiology and service-learning to increase science awareness and fostering the relationship between universities and the general public. Frontiers in Education
• Gimeno, A., Stanley, C.E., Ngamenie, Z., Hsung, M.H., Walder, F., Schieder, S.S., Bindschedler, S., Junier, P., Keller, B., & S. Vogelgsang, 2021. Fungi-on-a-Chip: A versatile microfluidic platform measures hyphal interactions between Fusarium graminearum and Clonostachys rosea in real-time. Communications Biology 4:262.
• Junier, P., Cailleau, G., Palmieri, I., Valloton, C., Trautschold, O., Junier, T., Paul, C., Bregnard, D., Palmieri, F., Estoppey, A., Buffi, M., Lohbgerger, A., Robinson, A., Kelliher, J., Davenport, K., House, G., Morales, D., Gallegos-Graves, L., Dichosa, A., Lupini, S., Nguyen, H., Young, J.D., Rodriguez, D., Parra-Vasquez, N., Bindschedler, S. & P.S. Chain. 2021. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiology Ecology 11;97:fiab003. Article selected as Editor’s choice.
• Dreier, M., Berthoud, H., Shani, N., Wechsler, D. & P. Junier. 2021. Development of a High-Throughput Microfluidic qPCR System for the Quantitative Determination of Quality-Relevant Bacteria in Cheese. Frontiers in microbiology 11:3391.
• Triki Z, Li Richter† X-Y, Demairé C, Kurokawa S, Bshary R, 2021. Marine cleaning mutualism defies standard logic of supply and demand. The American Naturalist (accepted)Xiang-Yi Li Richter*, Brian Hollis. Softness of selection and mating system interact to shape trait evolution under sexual conflict. Evolution, 75: 2335–2347.
• Li X-Y, Kokko H, 2021. Sexual dimorphism driven by intersexual resource competition: why is it rare, and where to look for it? Journal of Animal Ecology, 90: 1831–1843.
• Li X-Y, Morozov A, Goymann W, 2021. Coevolution of female fidelity and male help in populations with alternative reproductive tactics. Proceedings of the Royal Society B, 288: 20202371.
• Hausmann S, Gonzalez D, Geiser J, Valentini M, 2021. The DEAD-box RNA helicase RhlE2 is a global regulator of Pseudomonas aeruginosa lifestyle and pathogenesis, Nucleic Acids Research, 49.12, 6925–6940, https://doi.org/10.1093/nar/gkab503
• Krishna Kumar, R., Meiller-Legrand, T.A., Alcinesio, A. Gonzalez, D., et al. 2021. Droplet printing reveals the importance of micron-scale structure for bacterial ecology. Nat Commun 12, 857. https://doi.org/10.1038/s41467-021-20996-w
• Hervé, V., Simon, A., Randevoson, F., Cailleau, G., Rajoelison, G., Razakamanarivo, H., Bindschedler, S., Verrecchia, E., & P. Junier. 2021. Functional Diversity of the Litter-Associated Fungi from an Oxalate-Carbonate Pathway Ecosystem in Madagascar. Microorganisms, 9(5), 985.

• Joseph, E. & P. Junier. 2020. Metabolic processes applied to endangered metal and wood heritage objects: Call a microbial plumber! New Biotechnology, 56:21-26
• Palmieri, P., Palmieri, I., Noormamode, N., Estoppey, A., Ishak, M.O., Kelliher, J.M., Vallat, A., Iyer, R., Bindschedler, S., Davenport, K., Chain, P.S.G., Foster Harris, J. & P. Junier. Exploiting oxalotrophic bacteria to control Aspergillus niger lung infections. bioRxiv 2020.08.20.259929; doi: https://doi.org/10.1101/2020.08.20.259929
• Filippidou, S., Fatton, M., Junier, T., Berge, M., Poppleton, D., Blum, T.B., Kaminek, M., Odriozola, A., Blom, J., Johnson, S.L., Abrahams, J.P., Chain, P.S.G., Gribaldo, S., Tocheva, E.I., Zuber, B., Viollier, P.H. & P. Junier. Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. bioRxiv 2020.06.18.160689; doi: https://doi.org/10.1101/2020.06.18.160689.
• McGenity, T.J. Gessesse, A., Hallsworth, J.A., Garcia Cela, E., Verheecke-Vaessen, C., Wang, F., Chavarria, M., Haggblom, M.M., Molin, S., Danchin, A., Smid, E.J., Lood, C., Cockell, C.S., Whitby, C., Liu, S.L., Keller, N.P., Stein, L.Y., Bordenstein, S.R., Lal, R., Nunes, O.C., Gram, L., Singh, B.S., Webster, N.S., Morris, C., Sivinski, S., Bindschedler, S., Junier, P., Antunes, A., Baxter, B.K., Scavone, P. & K. Timmis. Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes. Microbial Biotechnology (2020) 0(0), 1–44.
• Dreier, M., Berthoud, H., Shani, N., Wechsler, D. & P. Junier. 2020. SpeciesPrimer: A bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species. PEERJ. 8:e854.
• Comensoli, L., Albini, M., Kooli, W.M., Maillard, J., Lombardo T., Junier, P. & E. Joseph. 2020. Investigation of Biogenic Passivating Layers on Corroded Iron. Materials, 13, 1176.
• Hashmi, I., S. Bindschedler & P. Junier. 2020. The Phylum Firmicutes. Beneficial Microbes in Agroecology, Volume I: Bacteria. Editors: N. Amaresan M. Senthil Kumar K. Annapurna Krishna Kumar A. Sankaranarayanan. Elsevier.
• Stelzl LS, Mavridou DA, Saridakis E, Gonzalez D, Baldwin AJ, Ferguson SJ, Sansom MS, Redfield C. Local frustration determines loop opening during the catalytic cycle of an oxidoreductase. Elife. 2020 Jun 22;9:e54661. doi: 10.7554/eLife.54661. PMID: 32568066; PMCID: PMC7347389.
• Woldemeskel SA, Daitch AK, Alvarez L, Panis G, Zeinert R, Gonzalez D, Smith E, Collier J, Chien P, Cava F, Viollier PH, Goley ED. The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter. PLoS Genet. 2020 Jan 21;16(1):e1008591. doi: 10.1371/journal.pgen.1008591. PMID: 31961855; PMCID: PMC6994171.
• Sandoz FA, Bindschedler S, Dauphin B, Farinelli L, Grant JR and Hervé V. 2020. Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae). Environmental Microbiology Reports. doi:10.1111/1758-2229.12840.

• Joseph E and Junier P. 2019. Metabolic processes applied to endangered metal and wood heritage objects: Call a microbial plumber! New Biotechnology, 2019
• Hashmi I, Paul C, Al-Dourobi A, Sandoz F, Deschamps P, Junier T, Junier P, Bindschedler S. 2019. Comparison of the plant growth-promotion performance of a consortium of Bacilli inoculated as endospores or as vegetative cells, FEMS Microbiology Ecology 95, 11, fiz147, doi:10.1093/femsec/fiz147
• Millière L, Gussone N, Moritz T, Bindschedler S, Verrecchia EP. 2019. Origin of strontium and calcium in pedogenic needle fibre calcite (NFC). Chemical Geology, 524, 329-344, doi : 10.1016/j.chemgeo.2019.06.022.
• Lohberger A, Spangenberg JE, Ventura Y, Bindschedler S, Verrecchia EP, Bshary R, Junier P. 2019. Effect of organic carbon and nitrogen on the interactions of Morchella spp. and bacteria dispersing on their mycelium. Frontiers in Microbiology – Fungi and Their Interactions, 10:124, doi: 10.3389/fmicb.2019.00124.
• Bindschedler S, Verrecchia EP. 2019. Fungal Weathering. In: Gargaud M et al. (eds) Encyclopedia of Astrobiology. Springer, Berlin, Heidelberg. doi:10.1007/978-3-642-27833-4_5400-1
• Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P. 2019. Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. In: Sariaslani S, Gadd GM (eds), Advances in Applied Microbiology, 106, doi.org/10.1016/bs.aambs.2018.10.001.
• Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P. 2019. Bacterial spores, from ecology to biotechnology. In: Sariaslani S, Gadd GM (eds), Advances in Applied Microbiology, 106, doi.org/10.1016/bs.aambs.2018.10.002.
• Blum, T., Filippidou, S., Hayoz, M., Junier, P., & J.P. Abrahams. 2019. The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo. Scientific Reports. 9: 14948.
• Filippidou, S., Junier, T., Wunderlin, T., Kooli, W.M., Palmieri, I., Al-dourobi, A., Molina, V., Lienhard, R., Spangenberg, J.E., Johnson, S.L., Chain, P.S, Dorador, C. & P. Junier. 2019. Adaptive strategies in a poly-extreme environment: differentiation of vegetative cells in Serratia ureilytica and resistance to extreme conditions. Frontiers in Microbiology. 10: 102.
• Kooli, W.M., Junier, T., Shakya, M., Monachon, M., Davenport, K.W., Vaideeswaran, K., Vernudachi, A., Marozau, I., Monrouzeau, T., Gleasner, C.D., McMurry, K., Leinhard, R., Rufener, L., Perret, J.L., Sereda, O., Chain, P.S., Joseph, E. & P. Junier. 2019. Remedial treatment of corroded iron objects by environmental Aeromonas isolates. Applied and Environmental Microbiology. 85: e02042-18. Selected for the Spotlight of the Biotechnology section.

• Blum, T., Filippidou, S., Hayoz, M., Junier, P. & J.P. Abrahams. The native structure of the flagellar filament of the Firmicute Kurthia at 3.0 Å resolution. 2019. Scientific Reports. 9: 14948.
• Paul, C., Bayrychenko, Z., Junier, T., Filippidou, S., Beck, K., Greub, G., Bürgmann, H. & P. Junier. 2018. Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PEERJ. Accepted.
• Losa G & Bindschedler S. 2018. Enhanced Tolerance to Cadmium in Bacterial-Fungal Co-Cultures as a Strategy for Metal Biorecovery from e-Waste. Minerals 8, 121, doi:10.3390/min8040121.
• Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. 2018. Bacterial – Fungal Interactions: ecology, mechanisms and challenges. FEMS Microbiology Reviews, fuy008, doi.org/10.1093/femsre/fuy008
• Pons S, Bindschedler S, Sebag D, Junier P, Verrecchia EP, Cailleau G. 2018. Biocontrolled soil nutrient distribution under the influence of an oxalogenic-oxalotrophic ecosystem. Plant and Soil. doi.org/10.1007/s11104-018-3573-1.
• Kooli, W.M., Comensoli, L., Maillard. J, Albini, M., Gelb, A., Junier, P.* & E. Joseph. 2018. Bacterial iron reduction and biogenic mineral formation for the stabilisation of corroded iron objects. Scientific Reports 8: 764. *Co-corresponding author.
• Madueño, L., Paul, C., Junier, T., Bayrychenko, Z., Filippidou, S., Beck, K., Greub, G., Bürgmann, H. & P. Junier. 2018. A historical legacy of antibiotic utilization on bacterial seed banks in sediments. PEERJ 6, e4197.
• Hervé, V., Clerc, M., Cailleau, G., Bueche, M., Junier, T., Verrecchia, E. & P. Junier. 2018. Carbonate accumulation in the bark of Terminalia bellirica: A new habitat for the oxalate-carbonate pathway. Geomicrobiology Journal 35: 31-39.
• Comensoli, L., Maillard, J., Albini, M., Sandoz, F., Junier, P.* & E. Joseph. 2018. Soluble and Solid Iron Reduction Assays with Desulfitobacterium hafniense. Bioprotocols. https://bio-protocol.org/e3002.
• Paul, C., Bayrychenko, Z., Junier, T., Filippidou, S., Beck, K., Greub, G., Bürgmann, H. & P. Junier. 2018. Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PEERJ. e4989.
• Albelda-Berenguer, M., Monachon, M., Jacquet, C., Junier, P., Remazeilles, C., Schofield, E. J. & E. Joseph. 2018. Biological oxidation of sulfur compounds in artificially degraded wood. International Biodeterioration & Biodegradation. 141: 62-70.
• Junier, P., Paul, C. & T. Junier. 2018. Le microbiote du sédiment : une approche novatrice pour tracer la consommation passée d’antibiotiques. Pipette SULM. 6 : 16-17.

• Bindschedler S, Bouquet Vu T, Job D, Joseph E, Junier P. 2017. Fungal biorecovery of gold from e-waste. Advances in Applied Microbiology 99, 53-81.
• Joseph E, Bindschedler S, Albini M, Comensoli L, Kooli W, Mathys L. 2017. Microorganisms for safeguarding cultural heritage, In «The Fungal Community: its Organization and Role in the Ecosystem (4th Edition), eds. Dighton J, White JF.
• Comensoli L, Bindschedler S, Junier P, Joseph E. 2017. Iron and fungal physiology: A review of biotechnological opportunities. Advances in applied microbiology 98, 31-60.
• Bergottini, V.M., Herve, V., Sosa, D.A., Otegui, M.B., Zapata, P.D. & P. Junier. 2017. Exploring the diversity of the root-associated microbiome of Ilex paraguariensis St. Hil (Yerba Mate). Applied Soil Ecology. 109: 23-31.
• Simon, A., Hervé, V., Al-Dourobi, A., Verrecchia, E. & P. Junier. 2017. An in situ inventory of fungi and their associated migrating bacteria in forest soils using fungal highways columns. FEMS Microbiology Ecology. 93:fiw217.
• Junier, P. & E. Joseph. 2017. Microbial biotechnology approaches to mitigating the deterioration of construction and heritage materials. Microbial Biotechnology. 10: 1145-1148.
• Comensoli, L., Maillard, J., Albini, M., Sandoz, F., Junier, P.* & E. Joseph. 2017. Use of bacteria to stabilize archaeological iron. Applied and Environmental Microbiology. 8:e03478-16 *Co-corresponding author.
• Fillippidou, S., Bindschedler, S., Jeanneret, N. & Junier P. 2017. Bacterial diversity in the sulfur and iron springs of Ponts-de-Martel, Neuchâtel. Bulletin de la Societe Neuchateloise de Sciences Naturelles.

• Bindschedler S, Cailleau G, Verrecchia EP. 2016. Role of Fungi in the biomineralization of calcite. Minerals 6 (2): 41, doi:10.3390/min6020041.
• Bueche M, P Junier. 2016. Effect of organic carbon and metal accumulation on the bacterial communities in sulphidogenic sediments. Environmental Science and Pollution Research 23, 10443–10456.
• Filippidou S, Bindschedler S, Jeanneret N, Junier P. 2016. Bacterial diversity in the sulfur and iron springs at ponts-de- martel, Neuchâtel. Bulletin de la Société Neuchâteloise des Sciences Naturelles 136, 37-49.
• Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Palmieri F, Palmieri I, Roussel-Delif L, Vieth-Hillebrand A, Vetter A, Chain PS, Regenspurg S & P Junier. 2016. Description of Anoxybacillus geothermalis sp. nov., an aerobic endospore-forming bacterium isolated from mineral deposits in the Groß Schönebeck geothermal station, Germany. International Journal of Systematic and Evolutionary Microbiology 66, 2944-51.
• Ganesan S, Fillipidou S, Junier T, Muñoz-Ruffat P, Jeanneret N, Wunderlin T, Sieber N, Dorador C & P Junier. 2016. Manganese-II oxidation and Copper-II resistance in endospore forming Firmicutes isolated from uncontaminated environmental sites. AIMS Environmental Science. 3: 220-238.
• Hervé V, Junier T, Bindschedler S, Verrecchia EP, Junier P. 2016. Diversity and ecology of oxalotrophic bacteria. World journal of microbiology & biotechnology 32(2).
• Wunderlin T, Junier T, Paul C, Jeanneret N, Junier P. 2016. Physical isolation of endospores from environmental samples by targeted lysis of vegetative cells. Journal of Visual Experiments. 107: e53411.
• Filipiddou, S., Wunderlin, T., Junier, T., Jeanneret, N., Dorador, C., Molina, V., Jonhson, D.R. & P. Junier. 2016. A combination of extreme environmental conditions favor the prevalence of Endospore-forming Firmicutes in geothermal and mineral springs. Frontiers in Microbiology. 7:1707.
• Andrés-Barrao, C., Saad, M.M., Cabello-Ferrete, E., Bravo, D., Chappuis, M.L., Ortega-Pérez, R., Junier, P., Perret, X. & F. Barja. 2016. Metaproteomics and ultrastructure characterization of Komagataeibacter spp. involved in high-acid spirit vinegar production. Food Microbiology. 55:112-122.
• Jacquet, S., Junier, P*., Zopfi, J., Brandl, H. & T. Curtis. 2016. Microbiologie. In: Dans les abysses du Leman. U. Lemmin. Presses polytechniques et universitaires romandes. * Editor of the chapter.

• Simon, A., Bindschedler, S., Job, D., Wick, L.Y., Filippidou, S., Kooli, W. M., Verrecchia, E.P. & P. Junier. 2015. Exploiting the fungal highway: Development of a novel tool for the in situ isolation of bacteria migrating along fungal mycelium. FEMS Microbiology Ecology 91(11).
• Filippidou, S., Jaussi, M., Junier, T., Wunderlin, T., Jeanneret, N., Regenspurg, S., Johnson, S., McMurry, K., Gleasner, C.D. Lo C-C., Li, P., Vuyisich, M., Chain, P.S. & P. Junier. Genome Sequence of Aeribacillus pallidus strain GS3372, an endospore-forming bacterium isolated in a deep geothermal reservoir. Genome Announcements. 3:e00982-15.
• Filippidou, S., Wunderlin, T., Junier, T., Jeanneret, N., Johnson, S., McMurry, K., Gleasner, C.D. Lo C-C., Li, P., Vuyisich, M., Chain, P.S. & P. Junier. 2015. Genome Announcement of Bacillus alveayuensis strain 24KAM51, a halotolerant thermophile isolated from a hydrothermal vent. Genome Announcements. 3:e00981-15.
• Wunderlin, T., Junier, T., Paul, C., Jeanneret, N. & P. Junier. 2015. Physical isolation of endospores from environmental samples by targeted lysis of vegetative cells. In press. Journal of Visual Experiments.
• Junier, T., Herve, V., Wunderlin, T. & P. Junier. 2015. MLgsc: a maximum-likelihood general sequence classifier. PLOSone.10: e0129384.
• Filippidou, S., Jaussi, M., Junier, T., Wunderlin, T., Roussel-Delif, L., Jeanneret, N., Vieth-Hillebrand A., Vetter, A., Regenspurg, S., Johnson, S., McMurry, K., Gleasner, C.D. Lo C-C., Li, P., Vuyisich, M., Chain, P.S. & P. Junier. 2015. Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a novel thermophilic endospore-forming species. Genome Announcements. 3: e00575-15.
• Filippidou, S., Junier, T., Wunderlin, T., Lo, CC., Li, P.E., Chain, P.S. & P. Junier. 2015. Under-detection of endospore-forming Firmicutes in metagenomic data. Computational and Structural Biotechnology Journal. 13: 299-306
• Bergottini, V.M., Otegui, M.B., Sosa, D.A., Zapata, P.D., Mulot, M., Rebord, M., Zopfi, J., Wiss, V.F., Benrey, B. & P. Junier. 2015. Bioinoculation of yerba mate seedlings (Ilex paraguariensis St. Hill) with native plant growth promoting rhizobacteria: a sustainable alternative to improve crop yield. In press. Biology and Fertility of Soils. 51:749-755
• Bergottini, V.M., Filippidou, S., Junier, T., Johnson, S., Chain, P., Otegui, M.B., Zapata, P.D., & P. Junier. 2015. Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacteria isolated from yerba mate (Ilex paraguariensis St. Hill.). Genome Announcements. 3: e00239-15.
• Bravo, D., Braissant, O., Cailleau, G., Verrecchia, E. & P. Junier. 2015. Isolation and characterization of oxalotrophic bacteria from tropical soils. Archives in Microbiology. 197: 65-77.

• Joseph, E., Albini, M., Letardi, P., Domon-Beuret, E., Brambilla, L., Mathys, L., Cevey, C., Bertholon, R., Job, D. & P. Junier. BIOPATINAS: Innovative biological patinas for copper-based artefacts. In Conference Proceedings of Outdoor Metallic Sculpture from the XIXth to the Beginning of the XXth Century: Identification, Conservation, Restoration. Paris, France. 4th-5th December 2014. ICOMOS France, Paris, 2014. In press.
• E. Joseph, P. Letardi, M. Albini, L. Comensoli, W. Kooli, L. Mathys, E. Domon Beuret, L. Brambilla, C. Cevey, R. Bertholon, D. Job, P. Junier. Innovative biological approaches for metal conservation. In Conference Proceedings of EUROCORR 2014, European Corrosion Congress. Pisa, Italy. 8th-12th September 2014. DECHEMA e.V., Frankfurt and AIM – Associazione Italiana di Metallurgia, Milano, 2014; ISBN 9783897461598, 1-10.
• E. Domon Beuret, L. Mathys, L. Brambilla, M. Albini, C. Cevey, R. Bertholon, P. Junier, E. Joseph. Biopatines: des champignons au service des alliages cuivreux. In Conference Proceedings of JOURNEES DES RESTAURATEURS EN ARCHEOLOGIE 2014 « restaurer l’ordinaire, exposer l’extraordinaire : du site au musée ». Arles, France. 16th-17th October 2014. Atelier de Conservation-Restauration du Musée Départemental Arles Antique (MDAA) et A-CORROS, Arles, 2014; in press.
• E. Joseph, M. Albini, P. Letardi, E. Domon Beuret, L. Brambilla, L. Mathys, C. Cevey, R. Bertholon, D. Job, P. Junier. BIOPATINAS: Innovative biological patinas for copper-based artefacts. In Conference Proceedings of Outdoor Metallic Sculpture from the XIXth to the Beginning of the XXth Century: Identification, Conservation, Restoration. Paris, France. 4th-5th December 2014. ICOMOS France, Paris, 2014; in press.
• Bindschedler S, Cailleau G, Braissant O, Millière L, Job D, Verrecchia EP. 2014. Unravelling the enigmatic origin of calcitic nanofibres in soils and caves: purely physicochemical or biogenic processes? Biogeosciences. 11, 2809-2825.
• Despland LM, Clark MW, Vancov T & M Aragno. 2014. Nutrient removal and microbial communities’ development in a young unplanted constructed wetland using Bauxsol™ pellets to treat wastewater. Science of the Total Environment. 484: 167-175
• Sauvain, L., Bueche, M., Junier, T., Masson, M., Wunderlin, T., Kohler-Milleret, R., Gascon-Diez, E., Loizeau, J.L., Tercier-Waeber, M.L. & P. Junier. 2014. Bacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria. Aquatic Sciences. 76: S33.
• Cailleau G, Mota M, Bindschedler S, Junier P & EP Verrecchia. 2014. Detection of active oxalate–carbonate pathway ecosystems in the Amazon Basin: Global implications of a natural potential C sink. Catena. 116: 132-141.
• Wunderlin, T., Corella, J.P., Junier, T., Bueche, M., Loizeau, J.L., Giradclos, S. & P. Junier. 2014. Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva, (Switzerland-France). Aquatic Sciences. 76: S103.
• Wunderlin, T., Junier, T., Roussel-Delif, L., Jeanneret, N. & P. Junier. 2014. Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments. Environmental Microbiology Reports. 6: 631-639.
• Junier, P., Alfaro, M., Guevara, R., Witzel K.P. & M. Caru. 2014. Genetic diversity of Rhizobium present in nodules of Phaseolus vulgaris L. cultivated in two soils of the central region in Chile. Applied Soil Ecology. 80: 60-66.

2013

• S. Gulzar, M. Wörle, J-P. Burg, M. Nawaz Chaudhry, E. Joseph, E. Reusser. Characterization of 17th Century Mughal tiles glazes from Shahdara Complex, Lahore-Pakistan. Journal of Cultural Heritage 2013, 14(2), 174-179.
• E. Joseph, D. Job, P. Junier, M. Wörle. MAIA: Microbes for Archaeological Iron Artefacts.Bulletin of research on metal conservation BROMEC 2013, 34, 5. Clic for publication
• Pion M, Spangenberg JE, Simon A, Bindschedler S, Flury C, Chatelain A, Bshary R, Job D & P Junier. 2013. Bacterial farming by the fungus Morchella crassipes. Proceedings of the Royal Society B. 208: 20132242.
• Bravo D, Cailleau G, Bindschedler S, Simon A, Job D, Verrecchia E & P Junier. 2013. Isolation of oxalotrophic bacteria able to disperse on fungal mycelium. FEMS Microbiology Letters. 348:157-166.
• Bravo, D., Martin, G., Maude, D., Cailleau, G., Verrechia, E. & P. Junier. 2013. Identification of active oxalotrophic bacteria by bromodeoxyuridine DNA-labeling in a microcosm soil experiment. FEMS Microbiology Letters. 348: 103-111.
• Pion, M., Bshary, R., Bindschedler, S., Filippidou, S., Wick, L. Y., Job, D. & P. Junier. 2013. Gains of bacterial flagellar motility in a fungal world. Applied and Environmental Microbiology.
• Wunderlin, T., Junier, T., Roussel-Delif, L., Jeanneret, N. & P. Junier. 2013. Stage 0 spurulation gene A (spo0A) as a molecular marker to study diversity of endospore-forming Firmicutes. Environmental Microbiology Reports. 5: 911-924.
• Joseph, E., Letardi, P., Comensoli, L., Simon, A., Junier, P., Job, D. & M. Woerle. Assessment of a biological approach for the protection of copper alloys artefacts. In Conference Proceedings of Metal 2013, Interim Meeting of the ICOM-CC Metal WG. Edinburgh, Scotland. 16th-20th September 2013. Historic Scotland, Edinburgh, 2013; ISBN 9781849171427, 203-207.
• Bueche, M., Wunderlin, T., Roussel-Delif, L., Junier, T., Sauvain, L., Jeanneret, N. & P. Junier. 2013. Quantification of endospore-forming Firmicutes by qPCR with the functional gene spo0A. Applied and Environmental Microbiology. 79: 5302-5312.
• Junier, P., Kim, O-S., Imhoff, J.F., Witzerl, K-P. & O. Hadas. 2013. Effect of salinity on cyanobacterial community composition along a transect from Fuliya spring into water of Lake Kinneret, Israel. Fundamental and Applied Limnology. 182 (2): 99-107.
• G. Sathiyanarayanan, G. Saibaba, G. Seghal Kiran, Joseph Selvin. Process optimization and production of polyhydroxybutyrate using palm jaggery as economical carbon source by marine sponge-associated Bacillus licheniformis MSBN12. In press. Bioprocess and Biosystems Engineering 36:1817-1827.
• G. Sathiyanarayanan, G. Seghal Kiran, Joseph Selvin. Synthesis of silver nanoparticles by polysaccharide bioflocculant produced from marine Bacillus subtilis MSBN17. 2013. Colloids and Surfaces B: Biointerfaces. 102: 13-20.

2012

• Martin, G., Guggiari, M., Bravo, D., Zopfi, J., Cailleau, G., Aragno, M., Job, D., Verrecchia, E., & P. Junier. 2012. Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction. Environmental Microbiology. 14(11):2960-70.
• Joseph E, Simon A, Mazzeo R, Job D and Wörle M. 2012. Spectroscopic characterization of an innovative biological treatment for corroded metal artefacts. Journal of Raman Spectroscopy. 43:1612-1616
• Bindschedler, S., Millière, L., Cailleau, G., Job, D. & E. P. Verrecchia. 2012. An ultrastructural approach to analogies between fungal structure and needle fibre calcite. Geomicrobiology Journal. 29:4 301-313.
• Joseph, E., Cario, S., Simon, A., Wörle, M., Mazzeo, R., Junier, P. & D. Job. 2012. Protection of metal artifacts with the formation of metal-oxalates complexes by Beauveria bassiana. Frontiers in Microbiology. 2: 1-8.
• Humbert, S., Zopfi, J. & S. Tarnawski. 2012. Abundance of anammox bacteria in different wetland soils. Environmental Microbiology Reports. 4(5): 484-490.
• Aragno M., Verrecchia E. 2012. The oxalate-carbonate pathway: a reliable sink for atmospheric CO2 through calcium carbonate biomineralization in ferralitic tropical soils. In: Satyanarayana, T. et al.: Microorganisms in environmental management. Springer Science + Business Media.

2011

• Mitchell, E.A.D., Belbahri, L., Job D., Pawlowski, J., Lara, E. 2011. Exploring the Terra incognita of unknown eukaryotic diversity in Soils – A major challenge we now have the tools to tackle! Bulletin BGS. 32: 57-62.
• Bravo, D., Braissant, O. Solokhina, M., Clerc, M., Daniels, A.U., Verrecchia, E. & P. Junier. 2011. Use of isothermal microcalorimetry assay to characterize microbial oxalotrophic activity. FEMS Microbiology Ecology. 78: 266-274.
• Guggiari, M., Bloque, R., Aragno, M., Verrecchia, E., Job, D. & P. Junier. 2011. Experimental calcium oxalate crystal production and dissolution by selected wood rot fungi. International Biodeterioration & Biodegradation. 65: 803-809.
• Junier, P., Dalla-Vecchia, E. & R. Bernier-Latmani. 2011. The response of Desulfotomaculum reducens MI-1 to U(VI) exposure: a transcriptomic study. Geomicrobiology Journal. 28:483-496.
• Joseph, E., Simon, A., Prati,S., Worle, M., Job, D. & R. Mazzeo. 2011. Development of an analytical procedure for evaluation of the protective behavior of innovative fungal patinas on archaeological and artistic metal artefacts. Analytical and Bioanalytical Chemistry 399: 2899-2907.
• Kim, O-S., Imhoff, J.F., Witzerl, K-P. & P. Junier. 2011. Distribution of nitrite reductase (nirK and nirS) genes in the water column and sediment-water interface of two lakes and the Baltic Sea. Aquatic Ecology. 45: 99-112.
• Mader, P., Kaiser, F., Adholeya, A., Singh, R., Uppal, H.S., Sharma, A.K., Srivastava, R., Sahai, V., Aragno, M., Wiemken, A., Johri, B.N. & P.M. Fried. 2011. Inoculation of root microorganisms for sustainable wheat-rice and wheat-black gram rotations in India. Soil Biology & Biochemistry. 43: 609-619.

2010

• Junier, P., Junier, T., Podell, S., Sims, D.R., Detter, J.C., Lykidis, A., Han, C.S., Wigginton, N.S., Gaasterland, T. & R. Bernier-Latmani. 2010. The genome of the spore-forming, metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environmental Microbiology. 12: 2738-2754.
• Beier, S., Kim, O-S., Junier, P., Bertilsson, S. & K-P. Witzel. 2010. Betaproteobacterial ammonia oxidizers in root zones of aquatic macrophytes. Fundamental and Applied Limnology. 177:241-255.
• Junier, P., Suvorova, E. I. & R. Bernier-Latmani. 2010. Effect of competing electron acceptors on uranium reduction by the bacterium Desulfotomaculum reducens strain MI-1. Geomicrobiology Journal. 27:435-443.
• Humbert, S., Tarnawski, S., Fromin, N., Mallet, M.P., Aragno, M. & Zopfi, J. 2010. Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity. Isme J. 4:450-454.
• Junier, P., Molina, V., Dorador, C., Hadas, O., Kim O.S., Junier, T., Witzel, K.P., & Imhoff, J.F. 2010. Functional and phylogenetic marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment. Applied Microbiology and Biotechnology. 85:425-440.
• Regenspurg, S., Roquier, C., Harfouche, M., Froidevaux, P., Steinmann, P., Junier, P., & R. Bernier-Latmani. 2010. Natural accumulation and binding form of uranium in an organic-rich soil of an alpine region (Switzerland). Geochimica et Cosmochimica Acta. 74: 2082-2098.
• Junier, P., Kim, O-S., Eckert, W., Casper, P., Imhoff, J.F., Witzel, K-P. & O. Hadas. 2010. Methane- and ammonia-oxidizing bacteria at the chemocline of Lake Kinneret. Aquatic Microbial Ecology. 58: 241-248.
• Bindschedler, S., Millière, L., Cailleau, G., Job, D., Verrecchia, E.P. 2010. Calcitic nanofibers in soils and caves: a putative fungal contribution to carbonatogenesis. Geological Society, London, Special Publications. 336: 225-238.
• Aragno, M., Verrecchia, E., Job, D., Cailleau, G., Braissant,O., Khammar, N., Ferro, K., Mota, M., Guggiari, M. & G. Martin. 2010. Calcium carbonate biomineralization in ferrallitic, tropical soils through the oxalate-carbonate pathway. Bulletin de la Société Suisse de Pédologie. 30, 127-130.
• Guggiari M., Bloque R., Aragno M., Verrecchia E.P. & D. Job. 2010. Role and dynamics of calcium oxalate production by selected Fungi. Bulletin de la Société Suisse de Pédologie. 30, 123-126.
• Srivastava, R., Aragno, M. & A.K. Sharma. 2010. Cow dung extract: a medium for the growth of pseudomonads enhancing their effi ciency as biofertilizer and biocontrol agent in rice. Indian Journal of Microbiology. 50, 349-354.

2009

• Junier, P., Frutschi, M., Wigginton, N.S., Schofield, E.J., Bargar, J.R. & R. Bernier-Latmani. 2009. Metal reduction by spores of Desulfotomaculum reducens. Environmental Microbiology. 11: 3007-3017.
• Junier, P., Caru, M. & K-P. Witzel. 2009. Effect of common bean (Phaseolus vulgaris L.) on the community composition of ammonia-oxidizing bacteria in soil. European Journal of Soil Biology. 41:252-258.
• Junier, P., Kim, O-S., Junier, T., Imhoff, J.F., Ahn, T-S. & K-P, Witzel. 2009. Using the amoCAB operon for community analysis in betaproteobacterial ammonia-oxidizing bacteria. Applied Microbiology and Biotechnology. 83:175-188.
• Junier, P., Junier, T., Witzel, K-P. & M. Caru, 2009. Composition of diazotrophic bacterial assemblages in bean-planted soil compared to unplanted soil. European Journal of Soil Biology. 45: 153-162.
• Abe Y, Aravena R, Zopfi J, Shouakar-Stash O, Cox E, Roberts JD, Hunkeler D. 2009. Carbon and Chlorine Isotope Fractionation during Aerobic Oxidation and Reductive Dechlorination of Vinyl Chloride and cis-1,2-Dichloroethene. Environmental Science and technology, 43: 101-107.
• Abe Y, Aravena R, Zopfi J, Shouakar-Stash O, Cox E, Roberts JD, Hunkeler D. 2009. Carbon and Chlorine Isotope Fractionation during Aerobic Oxidation and Reductive Dechlorination of Vinyl Chloride and cis-1,2-Dichloroethene. Environmental Science and technology, 43: 101-107.
• Abe Y, Zopfi, J, Hunkeler, D. 2009. Effect of molecule size on carbon isotope fractionation during biodegradation of chlorinated alkanes by Xanthobacter autotrophicus GJ10. Isotopes Isotopes in environmental and healt srudies, 45: 18-26.
• Khammar N, Martin G, Ferro K, Job D, Aragno M, Verrecchia E. 2009. Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil. Journal of microbiological methods, 76: 120-127.
• Pronk M, Goldscheider N, Zopfi J. 2009. Microbial communities in karst groundwater and their potential use for biomonitoring. Hydrogeology Journal, 17: 37-48.
• Sinreich M, Flynn R, Zopfi J. 2009. Use of particulate surrogates for assessing microbial mobility in subsurface ecosystems. Hydrogeology Journal, 17: 49-59.

2008

• Junier, P., Junier, T., & K-P. Witzel. 2008. TRiFLe: a program for in silico T-RFLP analysis with user-defined databases. Applied and Environmental Microbiology. 74:6452-6456.
• Kim, O-S., Junier, P., Imhoff, J.F. & K-P. Witzel. 2008. Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea. FEMS Microbiology Ecology. 66:367-378.
• Junier, P., Kim, O-S., Hadas, O., Imhoff, J.F. & K-P, Witzel. 2008. Experimental comparison of specific 16S rDNA primers for analyzing ammonia-oxidizing bacteria (AOB) in environmental samples. Applied and Environmental Microbiology. 74: 5231-5236.
• Junier, P., Kim, O-S., Witzel, K-P. Imhoff, J.F. & O. Hadas. 2008. Habitat-partitioning of denitrifying bacterial communities carrying nirS/nirK genes in the stratified water column of Lake Kinneret, Israel. Aquatic Microbial Ecology. 51: 129-140.
• Junier, P., Kim, O-S. Molina, V. Limburg, P. Junier, T. , Ihhoff, J.F. & K-P. Witzel. 2008. Comparative in silico analysis of PCR primers used for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria. FEMS Microbiology Ecology. 64: 141-152.
• Dhiaf, A., Junier, P., Bakhrouf, A. & K-P. Witzel. 2008. Resuscitation of ten-year VBNC Klebsiella oxytoca. Les Cahiers de Biologie Marine 49: 17-22.
• Job D. 2008. The mycorama centre: A new showcase for international mycology. International Journal of Medicinal Mushrooms, 10: 93-95.
• Kuffer N, Gillet F, Senn-Irlet B, Aragno M, Job D. 2008.Ecological eterminants of fungal diversity on deadwood in European Forests. Fungal Diversity, 30: 83-95.
• Weisskopf L, Le Bayon RC, Kohler F, Page V, Jossi M, Gobat JM, Martinoia E, Aragno M. 2008. Spatio-temporal dynamics of bacterial communities associated with two plant species differing in organic acid secretion: A one-year microcosm study on lupin and wheat. Soil Biology and Biochemistry, 40: 1772-1780.
• Zopfi J, Bttcher ME, Jorgensen BB. 2008. Biogeochemistry of sulfur and iron in Thioploca-colonized surface sediments in the upwelling area off central chile. Geochimica et Cosmochimica Acta, 72: 827-843.

2007

• Junier, P., Witzel K-P.. & O. Hadas. 2007. Genetic diversity of cyanobacterial communities in Lake Kinneret (Israel) using 16S rRNA gene, psbA and ntcA sequence analyses. Aquatic Microbial Ecology 49(3): 233-241.
• Kim, O-S., Junier, P., Imhoff, J. & K-P. Witzel. 2007. Comparative analysis of ammonia-oxidizing bacterial communities in two lakes in North Germany and the Baltic Sea. Archives in Hydrobiology 167: 335-350.
• Molina, V., Ulloa, O., Farías, L., Urrutia, H., Ramírez, S., Junier P. & K-P. Witzel. 2007. Ammonia-oxidizing b-proteobacteria from the oxygen minimum zone off northern Chile. Applied and Environmental Microbiology 73: 3547-3555.
• Fall S, Hamelin J, Ndiaye F, Assigbetse K, Aragno M, Chotte JL, Brauman A. 2007. Differences between bacterial communities in the gut of a soil-feeding termite (Cubitermes niokoloensis) and its mounds. Applied and Environmental microbiology, 73: 5199-5208.
• Goldscheider N, Haller L, Pote J, Wildi W, Zopfi J. 2007. Characterizing water circulation and contaminant transport in Lake Geneva using bacteriophage tracer experiments and limnological methods. Environmental Science and technology, 41, 5252-5258.
• Pronk M, Goldscheider N, Zopfi. 2007. Particle-size distribution as indicator for fecal bacteria contamination of drinking water from karst springs. Environmental Science and technology, 41: 8400-8405.

2006

• Imfeld G, Shani N, Roesti D, Fromin N, Johri BN, Gaur R, Rossi P, Locatelli L, Poly F, Aragno M. 2006. Diversity of phlD alleles in the rhizosphere of wheat cropped under annual rice-wheat rotation in fields of the Indo-Gangetic plains: influence of cultivation conditions. Current Science, 90: 1521-1525.
• Jossi M, Fromin N, Tarnawski S, Kohler F, Gillet F, Aragno M, Hamelin J. 2006. How elevated pCO2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions? FEMS Microbiology Ecology, 55: 339-350.
• Küffer N, and Senn-Irlet B. 2006. Influence of forest management on the species richness of wood-inhabiting basiomycetes ib Swiss forests. Biodiversity and conversation, in press Pronk M, Goldscheider N, Zopfi J. 2006. Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system. Hydrogeology Journal, 14: 473-484.
• Pronk M, Goldscheider N, Zopfi J. 2006. Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system. Hydrogeology Journal, 14: 473-484.
• Roesti D, Gaur R, Johri BN, Imfeld G, Sharma S, Kawaljeet K, Aragno M. 2006. Plant growth stage, fertiliser management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria affect the rhizobacterial community structure in rain-fed wheat fields. Soil Biology and Biochemistry, 38: 1111-1120.
• Tarnawski S, Hamelin J, Jossi M, Aragno M and Fromin N. 2006. Phenotypic structure of Pseudomonas populations is altered under elevated pCO2 in the rhizosphere of perennial grasses. Soil Biology and Biochemistry, 38(6): 1193-1201.
• Tarnawski S, Aragno M (2006). The influence of elevated pCO2 on functions and diversity of rhizosphere and soil bacterial communities. Chapter 22 in: Noesberger J, Long SP, Norby RJ, Stitt M Hendrey GH, Blum H (Eds): Managed Ecosystems and CO2- Case Studies, Processes and Perspectives. Series: Ecological Studies, Vol. 187 Springer, Berlin, Heidelberg.

2005

• Cailleau G, Braissant O, Dupraz C, Aragno M and Verrecchia EP. 2005. Biologically induced accumulations of CaCO3 in orthox soils of Biga, Ivory Coast. Catena 59: 1-17.
• Fromin N, Tarnawski S, Roussel-Delif L, Hamelin J, Baggs E.M, Aragno M. 2005. Nitrogen fertiliser rate affects the frequency of nitrate-dissimilating Pseudomonas spp. in the rhizosphere of Lolium perenne grown under elevated pCO2 (Swiss FACE). Soil Biology & Biochemestry 37: 1962-1965.
• Kohler F, Hamelin J, Gillet F, Gobat JM and Buttler A. 2005. Soil microbial community changes in wooded mountain pastures due to simulated effects of cattle grazing. Plant and Soil 278: 327-340.
• Küffer N and Senn-Irlet B. 2005. Diversity and ecology of wood-inhabiting basidiomycetes on fallen woody debris in various forest types in Switzerland. Mycological Progress 4(1): 77-86.
• Küffer N. 2005. Lobulicum occultum. Der Fleckenpilz. Schweiz. Zeitschrift für Pilzkunde 83 (4): 141-143.
• Nguyen-Queyrens A, Tarnawski S and Ceschia E. 2005. Growth and phosphorus productivity of non-mycorrhizal Pinus pinaster seedlings: Comparison of three populations and seven full-sib families within a population. Scandinavian Journal of Forest Research 20: 196-205.
• Pronk M., Goldscheider, N. and Zopfi, J. 2005. Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system – first results from the Yverdon test site (Switzerland). Hydrogeology Journal (published online, 11.6.05).
• Roesti D, Ineichen K, Braissant O, Redecker D, Wiemken A and Aragno M. 2005. Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum. Applied and Environmental Microbiology 71: 6673-6679.
• Roussel-Delif L, Tarnawski S, Hamelin J, Philippot L, Aragno M and Fromin N. 2005. Frequency and diversity of nitrate reductase genes among nitrate-dissimilating Pseudomonas in the rhizosphere of perennial grasses grown in field conditions. Microbial Ecology 49: 63-72.
• Tarnawski S, Hamelin J, Jossi M, Aragno M and Fromin N. 2005. Phenotypic structure of Pseudomonas populations is altered under elevated pCO2 in the rhizosphere of perennial grasses. Soil Biology and Biochemistry (Available online 11.10.05).
• Weisskopf L, Fromin N, Tomasi N, Aragno M and Martinoia E. 2005. Secretion activity of white lupin’s cluster roots influences bacterial abundance, function and community structure. Plant and soil 268 (1-2): 181-194.
• Wieland A, Zopfi J, Benthien A and Kuhl M. 2005. Biogeochemistry of an iron-rich hypersaline microbial mat (Camargue, France). Microbial Ecology 49: 34-49

2004

• Casali S and Job D. 2004. Isolement et identification par des méthodes culturales et moléculaire des souches d’Amillaria mellea dans les érables d’un parc public. Bull Soc Neuchâteloise de Sc. Nat. 127: 65-79.
• Flynn R, Hunkeler D, Guerin C, Burn C, Rossi P and Aragno M. 2004. Geochemical influences on H40/1 bacteriophage inactivation in glaciofluvial sands. Environmental Geology, 45(4): 504-518.
• Flynn R, Rossi P and Hunkeler D. 2004. Investigation of virus attenuation mechanisms in a fluvioglacial sand using column experiments. FEMS Microbiology Ecology 49: 83-95.
• Flynn R, Cornaton F, Hunkeler D and Rossi P. 2004. Bacteriophage transport through a fining-upwards sedimentary sequence: laboratory experiments and simulation. Journal of Contaminant Hydrology 74 (1-4): 231-252.
• Gaur R, Shani N, Jeet K, Johri BN, Rossi P and Aragno M. 2004. Diacetylphloroglucinol-producing pseudomonads do not influence AM fungi in wheat rhizosphere. Current Science India 86 (3): 453-457.
• Job D and Schiff-Giovannini I. 2004. Influence of strain and substrate formulation of culinary-medicinal maitake mushroom Grifola frondosa (Dicks.:Fr.) S.F.Gray (Aphyllophoromycetideae) on fruit body production. International Journal of Medicinal Mushrooms 6(1): 73-82.
• Job D. 2004. Optimization of wood fungal defibrillation using Gloeophyllum trabeum and Resinicium bicolor selected strains. Mycological Progress 3(2): 151-156.
• Job D. 2004. Use of coffee spent industry residues for pleurotus ostreatus production in solid state fermentation. Micologia 21 (4): 198-201.
• Küffer N and Senn-Irlet B. 2004. Holzbewohnende Pilze in europäischen Buchenwäldern. Projektbericht z.Hd. Abteilung Natur und Landschaft; Bundesamt für Umwelt, Wald und Landschaft, Bern. 33 pp.
• Roesti D, Fromin N, Rossi P, Oehl F, Ineichen K, Wiemken A and Aragno M. Effect of a natural arbuscular mycorrhizal fungi inoculum on the bacterial community in the wheat mycorrhizosphere and in the hyphosphere. in prep.
• Schiff-Giovannini I, Job D, Mambda A. 2004. Selection of Grifosa frondosa and Fomitopsis pinicola strains resistant to Trichoderma viride in teflon tubes confrontation method. Mycological Progress 3 (4): 324-336.
• Schiff-Giovannini I, Abou-Mansour E, Job D, Gillet F. 2004. Morphological, physiological and chemical variations in the cultivate edible and medicinal mushroom Grifola frondosa in regard to strain, substrate and technical treatments International Journal of Medicinal Mushrooms 6: 263-274.
• Zopfi J, Ferdelman TG and Fossing H. 2004. Distribution and fate of sulfur intermediates – sulfite, tetrathionate, thiosulfate and elemental sulfur – in marine sediments. In: « Sulfur Biogeochemistry – Past and present ». Editors: Amend J., Edwards K. and Lyons T., Geological Society of America, Boulder, Colorado. pp. 97-116.

2003

• Küffer N and Senn-Irlet B. 2003. Holzbewohnende Pilze in Schweizer Wäldern. Projektbericht z. Hd. Eidgenössische Forstdirektion; Bundesamt für Umwelt, Wald und Landschaft, Bern. 56 pp.
• Tarnawski S, Hamelin J, Locatelli L, Aragno M and Fromin N. 2003. Examination of Gould’s modified S1 (mS1) selective medium and Angle’s non-selective medium for collecting diversity of Pseudomonas spp. in soil and root environments. FEMS Microbiology and Ecology 45: 97-104.
• Wieland, A., Zopfi, J., Benthien, M. and Kühl, M. 2003. Biogeochemistry of an iron-rich microbial mat (Camargue, France): Oxygen, sulfur and carbon cycling. In: P. Caumette (ed.), Proceedings of the 3rd MATBIOPOL meeting, St. Raphael, 22-25 January, 2003

2002

• Braissant O, Verrechia E.P, Aragno M. 2002. Is the contribution of bacteria to terrestrial carbon budget greatly underestimated ? Naturwissenschaften 89: 366-370.
• Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M, and Rossi P. 2002. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environmental Microbiology 4(11): 634-643.
• Hamelin J, Fromin N, Tarnawski S, Teyssier-Cuvelle S, and Aragno M. 2002. nifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass. Environmental Microbiology 4(8): 477-481.
• Job D. 2002. Assessment of selected decay Basidiomycetes for selective biodefibrillation of Picea abies wood. Mycological Progress 1: 123-130.
• Langlade N.B, Messerli G, Weisskopf L, Plaza S, Tomasi N, Smutny J, Neumann G and Martinoia E. 2002. ATP citrate lyase: cloning, heterologous expression and possible implication in root organic acid metabolism and excretion. Plant, Cell and Environment. 25: 1561-1569.
• Locatelli L, Tarnawski S, Hamelin J, Rossi P, Aragno M, and Fromin N. 2002. Specific PCR amplification for the genus Pseudomonas targeting the 3′ half of 16S rDNA and the whole 16S-23S rDNA spacer. Systematic and Applied Microbiology 25(2): 220-227.
• Marschner P, Neumann G, Kania A, Weisskopf L and Lieberei R. 2002. Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.)
  Plant and Soil 246: 167-174.
• Morris C.E, Bardin M, Berge O, Frey-Klett P, Fromin N, Girardin H, Guinebretière M.-H, Lebaron P, Thiéry J, and Trousselier M. 2002. Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999. Microbiology and Molecular Biology Reviews 66(4): 592-616.
• Tamer A. Ü, Aragno M, and Sahin N. 2002. Isolation and characterization of a new type of aerobic, oxalic acid utilizing bacteria, and proposal of Oxalicibacterium flavum gen. nov., sp. nov. Systematic and Applied Microbiology 25 : 513-519.