Toutes les publications de l'équipe du laboratoire de Microbiologie sont listées sur cette page.

Les thèses de doctorat se trouvent ici : bibliothèque rero.doc

Bindschedler S, Bouquet Vu T, Job D, Joseph E, Junier P. Fungal biorecovery of gold from e-waste. Advances in Applied Microbiology 99, 53-81.

Filippidou S, Bindschedler S, Jeanneret N, Junier P. Bacterial diversity in the sulfur and iron springs at ponts-de- martel, Neuchâtel. Bulletin de la Société Neuchâteloise des Sciences Naturelles 136, 37-49.

Joseph E, Bindschedler S, Albini M, Comensoli L, Kooli W, Mathys L. 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. Iron and fungal physiology: A review of biotechnological opportunities. Advances in applied microbiology 98, 31-60.

Bindschedler S, Cailleau G, Verrecchia EP. 2016. Role of Fungi in the biomineralization of calcite. Minerals 6 (2): 41, doi:10.3390/min6020041.

Hervé V, Junier T, Bindschedler S, Verrecchia EP & P Junier. 2016. Diversity and ecology of oxalotrophic bacteria. World journal of microbiology & biotechnology 32(2).

Wunderlin, T., Junier, T., Paul, C., Jeanneret, N. & P. Junier. 2016. Physical isolation of endospores from environmental samples by targeted lysis of vegetative cells. Journal of Visual Experiments. 107: e53411.

Bueche, M. & P. Junier. 2016. Effect of organic carbon and metal accumulation on the bacterial communities in sulphidogenic sediments.

Ganesan, S., Fillipidou, S., Junier, T., Muñoz-Ruffat, P., Jeanneret, N., Wunderlin, T., Sieber, N., Dorador, C. & P. Junier. Manganese-II oxidation and Copper-II resistance in endospore forming Firmicutes isolated from uncontaminated environmental sites. AIMS Environmental Science. 3: 220-238.

Filippidou, S., Jaussi, M., Junier, T., Wunderlin, T., Jeanneret, N., Palmieri, F., Palmieri, I., Roussel-Delif, L., Vieth-Hillebrand A., Vetter, A., Chain, P.S., Regenspurg, S. & P. Junier. Description of Anoxybacillus geothermalis sp. nov., an aerobic endospore-forming bacterium isolated from mineral deposits in the Groß Schönebeck geothermal station, Germany. In press. International Journal of Systematic and Evolutionary Microbiology.

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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.

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.

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.


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.

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.

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.

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.

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.

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.

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

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.

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

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.

Hallenberg N & Küffer N. 2001. Long-distance spore dispersal in wood-inhabiting Basidomycetes. Nordic Journal of Botany 21: 431-436.

Hamelin J, Fromin N, Syed N, Teyssier-Cuvelle S, Duvanel N, and Aragno M. 2001. Inventaire moléculaire des bactéries fixatrices d'azote associées à la rhizosphère de Molinia coerulea. Bulletin de la Société Suisse de Pédologie 25: 35-40.

Jacquin J, Aragno M and Rossi P. 2001. Application of the bead-beater technique to the extraction of bacterial DNA from cheese samples. Milchwissenchaften 56: 563-565.

Job D & Giovannini I. 2001. Grifola frondosa Optimization of basidiocarp formation and study of its biological activities. International Journal of Medicinal Mushrooms 3: 164.

Job D & Giovannini I. 2001. Medicinal and edible mushrooms in Switzerland : development of culture techniques and pharmacological research. International Journal of Medicinal Mushrooms 3: 165.

Kennedy K, Müller I, Rossi P and Kozel R. 2001. Unconsolidated Rocks, p. 158-210. In Joanneum Research (ed.), Beiträge zur Hydrogeologie. Graz. 8th International Symposium on Water Tracing.

Küffer N & Senn-Irlet B. 2001. Wood decay and enzyme activities of green alder inhabiting fungi. Mycologia Helvetica 11: 153-167.

Lott Fischer J, Albrecht A and Kämpfer P. 2001. Mikrobiologie der Kompostierung von Abfällen, p. 1-39. In Springer (ed.), Biologische Behandlung organischer Abfälle. Berlin.

Rossi P, Kennedy K, Niehren S, Schnegg P-A, Müller I and Kinzelbach W. 2001. Results of bacteriophage, Microsphere and Solute Tracer Migration Comparison at Wilerwald Test Field. 2001. Switzerland, p. 180-210.

Weisskopf L, Fromin N, Martinoia E. and Aragno M. 2001. Bacterial diversity associated with the roots of White Lupin and interactions between plant and bacteria. Bulletin de la société suisse de pédologie. 25 :29-34.

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