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2019

Antibacterial polymer fibres by rosin compounding and melt-spinning

Kanerva, M., Puolakka, A., Takala, T. M., Elert, A. M., Mylläri, V., Jönkkäri, I., Sarlin, E., Seitsonen, J., Ruokolainen, J., Saris, P. & Vuorinen, J., 8 May 2019, In : Materials Today Communications.

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Antibiotic Resistance Genes in the Human-Impacted Environment: A One Health Perspective

Tiedje, J. M., Wang Fang, Manaia, C. M., Virta, M., Sheng Hongjie, Ma Liping, Zhang Tong & Topp, E., Jun 2019, In : Pedosphere. 29, 3, p. 273-282 10 p.

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Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

Parnanen, K. M. M., Narciso-da-Rocha, C., Kneis, D., Berendonk, T. U., Cacace, D., Thi Thuy Do, Elpers, C., Fatta-Kassinos, D., Henriques, I., Jaeger, T., Karkman, A., Luis Martinez, J., Michael, S. G., Michael-Kordatou, I., O'Sullivan, K., Rodriguez-Mozaz, S., Schwartz, T., Sheng, H., Sorum, H., Stedtfeld, R. D. & 6 othersTiedje, J. M., Varela Della Giustina, S., Walsh, F., Vaz-Moreira, I., Virta, M. & Manaia, C. M., Mar 2019, In : Science Advances. 5, 3, 10 p., 9124.

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Dehydroabietylamine-Based Cellulose Nanofibril Films: A New Class of Sustainable Biomaterials for Highly Efficient, Broad-Spectrum Antimicrobial Effects

Hassan, G. A. M. S., Forsman, N., Wan, X., Keurulainen, L., Bimbo, L. M., Johansson, L-S., Sipari, N., Yli-Kauhaluoma, J. T., Zimmermann, R., Stehl, S., Werner, C., Saris, P. E. J., Österberg, M. & Moreira, V. M., 4 Mar 2019, In : ACS Sustainable Chemistry & Engineering. 7, 5, p. 5002-5009 8 p.

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Draft genome sequences of three monokaryotic isolates of the white-rot basidiomycete fungus Dichomitus squalens

Casado López, S., Peng, M., Daly, P., Andreopoulos, B., Pangilinan, J., Lipzen, A., Riley, R., Ahrendt, S., Ng, V., Barry, K., Daum, C., Grigoriev, I. V., Hilden, S. K., Mäkelä, M. R. & de Vries, R. P., 2019, (Accepted/In press) In : Microbiology Resource Announcements.

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Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments

Karkman, A., Parnanen, K. & Larsson, D. G. J., 8 Jan 2019, In : Nature Communications. 10, 8 p., 80.

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Field-compatible protocol for detecting tetracyclines with bioluminescent bioreporters without pipetting steps

Muurinen, J., Pasupulate, A., Lappalainen, J. & Virta, M., Mar 2019, In : Luminescence. 34, 2, p. 249-254 6 p.

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Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

Mäkinen, M., Kuuskeri, J., Laine, P., Smolander, O-P., Kovalchuk, A., Zeng, Z., Asiegbu, F., Paulin, L., Auvinen, P. & Lundell, T., 28 May 2019, In : BMC Genomics. 20, 22 p., 430.

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Identification and structural analysis of cereal arabinoxylan-derived oligosaccharides by negative ionization HILIC-MS/MS

Juvonen, M. K., Kotiranta, M., Jokela, J. K., Tuomainen, P. & Tenkanen, T. M., 1 Mar 2019, In : Food Chemistry. 275, p. 176-185 10 p.

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Interaction between tannins and fungal necromass stabilizes fungal residues in boreal forest soils

Adamczyk, B., Sietio, O-M., Biasi, C. & Heinonsalo, J., Jul 2019, In : New Phytologist. 223, 1, p. 16-21 6 p.

Research output: Contribution to journalArticleScientific

Midbiotics: conjugative plasmids for genetic engineering of natural gut flora

Ruotsalainen, P., Penttinen, R., Mattila, S. & Jalasvuori, M., 5 Apr 2019, In : Gut Microbes. p. 1-11 11 p.

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Occurrence of sul and tet(M) genes in bacterial community in Japanese marine aquaculture environment throughout the year: Profile comparison with Taiwanese and Finnish aquaculture waters

Suzuki, S., Nakanishi, S., Tamminen, M., Yokokawa, T., Sato-Takabe, Y., Ohta, K., Chou, H-Y., Muziasari, W. I. & Virta, M., 15 Jun 2019, In : Science of the Total Environment. 669, p. 649-656 8 p.

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The Biosynthesis of Rare Homo-Amino Acid Containing Variants of Microcystin by a Benthic Cyanobacterium

Shishido, T. K., Jokela, J., Humisto, A., Suurnäkki, S., Wahlsten, M., Oliveria de Alvarenga, D., Sivonen, K. & Fewer, D., 7 May 2019, In : Marine Drugs. 17, 5, p. 1 16 p.

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The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum

Coconi Linares, N., Di Falco, M., Benoit, I., Gruben, B., Peng, M., Tsang, A., Mäkelä, M. R. & de Vries, R., 2019, In : New Biotechnology.

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Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR

Qin, H., Wang, S., Feng, K., He, Z., Virta, M. P. J., Hou, W., Dong, H. & Deng, Y., 4 May 2019, In : Microbiome. 7, 12 p., 71.

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2018

Alternative biosynthetic starter units enhance the structural diversity of cyanobacterial lipopeptides

Mareš, J., Hajek, J., Urajova, P., Kust, A., Jokela, J. K., Saurav, K., Galica, T., Čapková, K., Mattila, A. I., Haapaniemi, E., Permi, P., Mysterud, I., Skulberg, O., Karlsen, J., Fewer, D. P., Sivonen, A. K., Tønnesen, H. & Hrouzek, P., 28 Nov 2018, (Accepted/In press) In : Applied and Environmental Microbiology. AEM02675-18R1 .

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Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms

Rinta-Kanto, J. M., Pehkonen, K., Sinkko, H., Tamminen, M. V. & Timonen, S., Oct 2018, In : Canadian Journal of Microbiology. 64, 10, p. 716-726 11 p.

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Biosynthesis of microcystin hepatotoxins in the cyanobacterial genus Fischerella

Heck, K., Alvarenga, D. O., Shishido, T. K., Varani, A. M., Dorr, F. A., Pinto, E., Rouhiainen, L., Jokela, J., Sivonen, K. & Fiore, M. F., Jan 2018, In : Toxicon. 141, p. 43-50 8 p.

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Black Queen Evolution and Trophic Interactions Determine Plasmid Survival after the Disruption of the Conjugation Network

Cairns, J., Koskinen, K., Penttinen, R., Patinen, T., Hartikainen, A., Jokela, R., Ruusulehto, L., Viitamäki, S., Mattila, S., Hiltunen, T. & Jalasvuori, M., 2 Oct 2018, In : mSystems. 3, 5, 14 p., e00104-18.

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Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the carbohydrate-active enzymes (CAZy) database

Mäkelä, M. R., Dilokpimol, A., Koskela, S. M., Kuuskeri, J., de Vries, R. P. & Hilden, K., Sep 2018, In : Microbial Biotechnology. 11, 5, p. 869-880 12 p.

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Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the CAZy database

Mäkelä, M. R., Dilokpimol, A., Koskela, S. M., Kuuskeri, J. T., de Vries, R. & Hilden, S. K., 2018, (Accepted/In press) In : Microbial Biotechnology.

Research output: Contribution to journalArticleScientificpeer-review

Co-expression of Nisin Z and Leucocin C as a Basis for Effective Protection Against Listeria monocytogenes in Pasteurized Milk

Fu, Y., Qiao, W., Zhu, D., Wang, X., Liu, F., Xu, H., Saris, P. E. J., Kuipers, O. & Qiao, M., 23 Mar 2018, In : Frontiers in Microbiology. 2018 / 9 , p. 1 - 11 11 p., 547.

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Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes

Peng, M., Aguilar-Pontes, M. V., Hainaut, M., Henrissat, B., Hilden, K., Mäkelä, M. R. & de Vries, R. P., Mar 2018, In : Fungal Genetics and Biology. 112, p. 40-46 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity

Teikari, J. E., Hou, S., Wahlsten, M., Hess, W. R. & Sivonen, K., 8 Mar 2018, In : Frontiers in Microbiology. 9, 13 p., 356.

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Construction and characterization of synthetic bacterial community for experimental ecology and evolution

Cairns, J., Jokela, R., Hultman, J., Tamminen, M., Virta, M. & Hiltunen, T., 14 Aug 2018, In : Frontiers in Genetics. 9, 12 p., 312.

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Contribution of YthA, a PspC family transcriptional regulator to Lactococcus lactis F44 acid tolerance and nisin yield: a transcriptomic approach

Wu, H., Liu, J., Miao, S., Zhao, Y., Zhu, H., Qiao, M., Saris, P. E. J. & Qiao, J., Mar 2018, In : Applied and Environmental Microbiology. 84, 6, p. 1-20 20 p., UNSP e02483-17.

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Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change

Markussen, T., Happel, E. M., Teikari, J. E., Huchaiah, V., Alneberg, J., Andersson, A. F., Sivonen, A. K., Riemann, L., Middelboe, M. & Kisand, V., 1 Aug 2018, In : Environmental Microbiology. 20, 8, p. 3083-3099 17 p.

Research output: Contribution to journalArticleScientificpeer-review

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

Daly, P., Lopez, S. C., Peng, M., Lancefield, C. S., Purvine, S. O., Kim, Y-M., Zink, E. M., Dohnalkova, A., Singan, V. R., Lipzen, A., Dilworth, D., Wang, M., Ng, V., Robinson, E., Orr, G., Baker, S. E., Bruijnincx, P. C. A., Hilden, K. S., Grigoriev, I. V., Mäkelä, M. R. & 1 othersde Vries, R. P., Nov 2018, In : Environmental Microbiology. 20, 11, p. 4141-4156 16 p.

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Discovery of a Pederin Family Compound in a Nonsymbiotic Bloom-Forming Cyanobacterium

Kust, A., Mares, J., Jokela, J., Urajova, P., Hajek, J., Saurav, K., Voracova, K., Fewer, D. P., Haapaniemi, E., Permi, P., Rehakova, K., Sivonen, K. & Hrouzek, P., May 2018, In : ACS Chemical Biology. 13, 5, p. 1123-1129 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Disruption of the methionine cycle and reduced cellular gluthathione levels underlie potex-potyvirus synergism in Nicotiana benthamiana

De, S., Chavez-Calvillo, G., Wahlsten, M. & Mäkinen, K., Aug 2018, In : Molecular Plant Pathology. 19, 8, p. 1820-1835 16 p.

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Draft genome sequence of the basidiomycete white-rot fungus Phlebia centrifuga

Mäkelä, M. R., Peng, M., Granchi, Z., Chin-A-Woeng, T., Hegi, R., van Pelt, S., Ahrendt, S., Riley, R., Heinaut, M., Henrissat, B., Grigoriev, I., de Vries, R. & Hilden, S. K., Apr 2018, In : Genome Announcements. 6, 14, 2 p., UNSP e01414-17.

Research output: Contribution to journalArticleScientificpeer-review

Dual-stressor selection alters eco-evolutionary dynamics in experimental communities

Hiltunen, T., Cairns, J., Frickel, J., Jalasvuori, M., Laakso, J., Kaitala, V., Kuenzel, S., Karakoc, E. & Becks, L., Dec 2018, In : Nature Ecology & Evolution. 2, 12, p. 1974-1981 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes

Cairns, J., Ruokolainen, L., Hultman, J., Tamminen, M., Virta, M. & Hiltunen, T., 19 Apr 2018, In : Communications Biology. 1, 8 p., 35.

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Effect of resource availability on evolution of virulence and competition in an environmentally transmitted pathogen

Pulkkinen, K., Pekkala, N., Ashrafi, R., Hamalainen, D. M., Nkembeng, A. N., Lipponen, A., Hiltunen, T., Valkonen, J. K. & Taskinen, J., May 2018, In : FEMS Microbiology Ecology. 94, 5, 12 p., 060.

Research output: Contribution to journalArticleScientificpeer-review

Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios

Rodríguez, J., Gallampois, C. M. J., Timonen, S., Andersson, A., Sinkko, H., Haglund, P., Berglund, Å. M. M., Ripszam, M., Figueroa, D., Tysklind, M. & Rowe, O., 30 Nov 2018, In : Frontiers in Microbiology. 9, 21 p., 2926.

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Ericoid plant species and Pinus sylvestris shape fungal communities in their roots and surrounding soil

Sietio, O-M., Tuomivirta, T., Santalahti, M., Kiheri, H., Timonen, S., Sun, H., Fritze, H. & Heinonsalo, J., Apr 2018, In : New Phytologist. 218, 2, p. 738-751 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Frequency of virus-resistant hosts determines experimental community dynamics.

Coloma, S. E., Gaedge, U., Sivonen, A. K. & Hiltunen, T. J., 28 Nov 2018, (Accepted/In press) In : Ecology. p. 1-9 9 p., ECY2554.

Research output: Contribution to journalArticleScientificpeer-review

Fungal feruloyl esterases: Functional validation of genome mining based enzyme discovery including uncharacterized subfamilies

Dilokpimol, A., Mäkelä, M. R., Varriale, S., Zhou, M., Cerullo, G., Gidijala, L., Hinkka, H. T., Brás, J. L. A., Jütten, P., Piechot, A., Verhaert, R., Hilden, S. K., Faraco, V. & de Vries, R., 2018, In : New Biotechnology. 41, p. 9-14 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization

Dilokpimol, A., Makela, M. R., Cerullo, G., Zhou, M., Varriale, S., Gidijala, L., Bras, J. L. A., Jutten, P., Piechot, A., Verhaert, R., Faraco, V., Hilden, K. S. & de Vries, R. P., 25 Jan 2018, In : New Biotechnology. 40, Part B, p. 282-287 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Mäkelä, M. R., Di Falco, M., McDonnell, E., Nguyen, T. T. M., Wiebenga, A., Hilden, S. K., Peng, M., Grigoriev, I. V., Tsang, A. & de Vries, R. P., Sep 2018, In : Studies in Mycology. 91, p. 79-99 21 p.

Research output: Contribution to journalArticleScientificpeer-review

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Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales)

Urquhart, A., Mondo, S., Mäkelä, M. R., Hane, J., Wiebenga, A., He, G., Mihaltcheva, S., Pangilinan, J., Lipzen, A., Barry, K., de Vries, R., Grigoriev, I. V. & Idnurm, A., 13 Dec 2018, In : Frontiers in Microbiology. 9, 21 p., 3058.

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Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent

Hultman, J., Tamminen, M., Pärnänen, K., Cairns, J., Karkman, A. & Virta, M., 1 Apr 2018, In : FEMS Microbiology Ecology. 94, 4, p. 1-10 10 p., fiy038.

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Indoor Trichoderma strains emitting peptaibols in guttation droplets

Castagnoli, E., Marik, T., Mikkola, R., Kredics, L., Andersson, M. A., Salonen, H. & Kurnitski, J., Nov 2018, In : Journal of Applied Microbiology. 125, 5, p. 1408-1422 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens

Lopez, S. C., Peng, M., Issak, T. Y., Daly, P., de Vries, R. P. & Mäkelä, M. R., Jun 2018, In : Applied and Environmental Microbiology. 84, 11, 11 p., e00403-18.

Research output: Contribution to journalArticleScientificpeer-review

Influence of allochthonous dissolved organic matter on pelagic basal production in a northerly estuary

Andersson, A., Brugel, S., Paczkowska, J., Rowe, O. F., Figueroa, D., Kratzer, S. & Legrand, C., 1 May 2018, In : Estuarine, Coastal and Shelf Science. 204, p. 225-235 11 p.

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In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics

Peng, M., Aguilar-Pontes, M. V., de Vries, R. P. & Mäkelä, M. R., 18 May 2018, In : Frontiers in Microbiology. 9, 10 p., 1045.

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Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Vesth, T. C., Nybo, J. L., Theobald, S., Frisvad, J. C., Larsen, T. O., Nielsen, K. F., Hoof, J. B., Brandl, J., Salamov, A., Riley, R., Gladden, J. M., Phatale, P., Nielsen, M. T., Lyhne, E. K., Kogle, M. E., Strasser, K., McDonnell, E., Barry, K., Clum, A., Chen, C. & 18 othersLaButti, K., Haridas, S., Nolan, M., Sandor, L., Kuo, A., Hainaut, M., Drula, E., Tsang, A., Magnuson, J. K., Henrissat, B., Wiebenga, A., Simmons, B. A., Makela, M. R., de Vries, R. P., Grigoriev, I. V., Mortensen, U. H., Baker, S. E. & Andersen, M. R., Dec 2018, In : Nature Genetics. 50, 12, p. 1688-1695

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Lignocellulose bioconversion to ethanol by a fungal single-step consolidated method tested with waste substrates and co-culture experiments

Mattila, H. K., Kačar, D., Mali, T. L. E. & Lundell, T. K., 18 Oct 2018, In : AIMS Energy. 6, 5, p. 866-879 14 p.

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