Publications of the Environmental Genomics and Systems Biology Research Group | ZHAW Institute of Natural Resource Sciences IUNR

Fernandes, Camila; Martins, Leonor; Teixeira, Miguel; Blom, Jochen; Pothier, Joël; Fonseca, Nuno A.; Tavares, Fernando,

2021.

Comparative genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis strains isolated from a single walnut host tree.

Microorganisms.

9(3),

pp.624.

Available from: https://doi.org/10.3390/microorganisms9030624

Doolotkeldieva, Tinatin; Bobushova, Saikal; Carnal, Simon; Rezzonico, Fabio,

2021.

Genetic characterization of Erwinia amylovora isolates detected in the wild walnut‑fruit forest of South Kyrgyzstan.

Journal of Plant Pathology.

Available from: https://doi.org/https://doi.org/10.1007/s42161-021-00752-1

Schmautz, Zala; Espinal, Carlos A.; Smits, Theo H. M.; Frossard, Emmanuel; Junge, Ranka,

2021.

Nitrogen transformations across compartments of an aquaponic system.

Aquacultural Engineering.

92(102145).

Available from: https://doi.org/10.1016/j.aquaeng.2021.102145

Schmautz, Zala; Espinal, Carlos A.; Bohny, Andrea M.; Rezzonico, Fabio; Junge, Ranka; Frossard, Emmanuel; Smits, Theo H. M.,

2021.

Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments.

BMC Microbiology.

21(12).

Available from: https://doi.org/10.1186/s12866-020-02075-0

Puławska, Joanna; Kałużna, Monika; Warabieda, Wojciech; Pothier, Joël F.; Gétaz, Michael; van der Wolf, Jan M.,

2020.

Transcriptome analysis of Xanthomonas fragariae in strawberry leaves.

Scientific Reports.

10(20582).

Available from: https://doi.org/10.1038/s41598-020-77612-y

Gaganidze, Dali; Sadunishvili, Tinatin; Aznarashvili, Mariam; Abashidze, Ekaterine; Gurielidze, Manana; Carnal, Simon; Rezzonico, Fabio; Zubadalashvili, Manana,

2020.

Fire blight distribution in Georgia and characterization of selected Erwinia amylovora isolates.

Journal of Plant Pathology.

Available from: https://doi.org/10.1007/s42161-020-00700-5

Murray, Alison E.; Freudenstein, John; Gribaldo, Simonetta; Hatzenpichler, Roland; Hugenholtz, Philip; Kämpfer, Peter; Konstantinidis, Konstantinos T.; Lane, Christopher E.; Papke, R. Thane; Parks, Donovan H.; Rossello-Mora, Ramon; Stott, Matthew B.; Sutcliffe, Iain C.; Thrash, J. Cameron; Venter, Stephanus N.; Whitman, William B.; Acinas, Silvia G.; Amann, Rudolf I.; Anantharaman, Karthik; Armengaud, Jean; Baker, Brett J.; Barco, Roman A.; Bode, Helge B.; Boyd, Eric S.; Brady, Carrie L.; Carini, Paul; Chain, Patrick S. G.; Colman, Daniel R.; DeAngelis, Kristen M.; de los Rios, Maria Asuncion; Estrada-de los Santos, Paulina; Dunlap, Christopher A.; Eisen, Jonathan A.; Emerson, David; Ettema, Thijs J. G.; Eveillard, Damien; Girguis, Peter R.; Hentschel, Ute; Hollibaugh, James T.; Hug, Laura A.; Inskeep, William P.; Ivanova, Elena P.; Klenk, Hans-Peter; Li, Wen-Jun; Lloyd, Karen G.; Löffler, Frank E.; Makhalanyane, Thulani P.; Moser, Duane P.; Nunoura, Takuro; Palmer, Marike; Parro, Victor; Pedrós-Alió, Carlos; Probst, Alexander J.; Smits, Theo; Steen, Andrew D.; Steenkamp, Emma T.; Spang, Anja; Stewart, Frank J.; Tiedje, James M.; Vandamme, Peter; Wagner, Michael; Wang, Feng-Ping; Yarza, Pablo; Hedlund, Brian P.; Reysenbach, Anna-Louise,

2020.

Author correction : roadmap for naming uncultivated archaea and bacteria.

Nature Microbiology.

6(1),

pp.136.

Available from: https://doi.org/10.1038/s41564-020-00827-2

Dia, Nay C.; Rezzonico, Fabio; Smits, Theo H. M.; Pothier, Joël F.,

2020.

Complete or high-quality draft genome sequences of six Xanthomonas hortorum strains sequenced with short- and long-read technologies.

Microbiology Resource Announcements.

9(41),

pp.e00828-20.

Available from: https://doi.org/10.1128/MRA.00828-20

Martins, Leonor; Fernandes, Camila; Blom, Jochen; Dia, Nay C.; Pothier, Joël F.; Tavares, Fernando,

2020.

Xanthomonas euroxanthea sp. nov. : a new xanthomonad species including pathogenic and non-pathogenic strains of walnut.

International Journal of Systematic and Evolutionary Microbiology.

70(12),

pp.6024-6031.

Available from: https://doi.org/10.1099/ijsem.0.004386

Kaufmann, Moritz; Schüle, Martin; Smits, Theo; Pothier, Joël,

2020.

Typing plasmids with distributed sequence representation [paper].

In:

Schilling, Frank-Peter; Stadelmann, Thilo, eds.,

Artificial Neural Networks in Pattern Recognition.

9th IAPR TC 3 Workshop on Artificial Neural Networks for Pattern Recognition (ANNPR'20), Winterthur, Switzerland, 2-4 September 2020.

Cham:

Springer.

pp.200-210.

Lecture Notes in Computer Science ; 12294.

Available from: https://doi.org/10.1007/978-3-030-58309-5_16

Gétaz, Michael; Puławska, Joanna; Smits, Theo H.M.; Pothier, Joël F.,

2020.

Host–pathogen interactions between Xanthomonas fragariae and its host Fragaria × ananassa investigated with a dual RNA-Seq analysis.

Microorganisms.

8(8),

pp.1253.

Available from: https://doi.org/10.3390/microorganisms8081253

Gétaz, Michael; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

2020.

Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations.

Phytopathology Research.

2020(2),

pp.17.

Available from: https://doi.org/10.1186/s42483-020-00061-y

Escursell, Mireia Marcé; Roschi, Alexia; Smits, Theo; Rezzonico, Fabio,

2020.

Characterization and direct molecular discrimination of rpsL mutations leading to high streptomycin resistance in Erwinia amylovora.

Journal of Plant Pathology.

Available from: https://doi.org/10.1007/s42161-020-00600-8

Murray, Alison E.; Freudenstein, John; Gribaldo, Simonetta; Hatzenpichler, Roland; Hugenholtz, Philip; Kämpfer, Peter; Konstantinidis, Konstantinos T.; Lane, Christopher E.; Papke, R. Thane; Parks, Donovan H.; Rossello-Mora, Ramon; Stott, Matthew B.; Sutcliffe, Iain C.; Thrash, J. Cameron; Venter, Stephanus N.; Whitman, William B.; Acinas, Silvia G.; Amann, Rudolf I.; Anantharaman, Karthik; Armengaud, Jean; Baker, Brett J.; Barco, Roman A.; Bode, Helge B.; Boyd, Eric S.; Brady, Carrie L.; Carini, Paul; Chain, Patrick S. G.; Colman, Daniel R.; DeAngelis, Kristen M.; de los Rios, Maria Asuncion; Estrada-de los Santos, Paulina; Dunlap, Christopher A.; Eisen, Jonathan A.; Emerson, David; Ettema, Thijs J. G.; Eveillard, Damien; Girguis, Peter R.; Hentschel, Ute; Hollibaugh, James T.; Hug, Laura A.; Inskeep, William P.; Ivanova, Elena P.; Klenk, Hans-Peter; Li, Wen-Jun; Lloyd, Karen G.; Löffler, Frank E.; Makhalanyane, Thulani P.; Moser, Duane P.; Nunoura, Takuro; Palmer, Marike; Parro, Victor; Pedrós-Alió, Carlos; Probst, Alexander J.; Smits, Theo H.M.; Steen, Andrew D.; Steenkamp, Emma T.; Spang, Anja; Stewart, Frank J.; Tiedje, James M.; Vandamme, Peter; Wagner, Michael; Wang, Feng-Ping; Hedlund, Brian P.; Reysenbach, Anna-Louise,

2020.

Roadmap for naming uncultivated archaea and bacteria.

Nature Microbiology.

5,

pp.987-994.

Available from: https://doi.org/10.1038/s41564-020-0733-x

Rothen, Julian; Sapugahawatte, Dulmini Nanayakkara; Li, Carmen; Lo, Norman; Vogel, Guido; Foucault, Frédéric; Pflüger, Valentin; Pothier, Joël; Blom, Jochen; Daubenberger, Claudia; Ip, Margaret,

2020.

A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS.

Scientific Reports.

10(8788).

Available from: https://doi.org/10.1038/s41598-020-65707-5

Madhaiyan, Munusamy; Saravanan, Venkatakrishnan Sivaraj; Blom, Jochen; Smits, Theo; Rezzonico, Fabio; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Whitman, William B.; Ji, Lianghui,

2020.

Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.).

International Journal of Systematic and Evolutionary Microbiology.

70(2),

pp.841-848.

Available from: https://doi.org/10.1099/ijsem.0.003834

Fossou, Romain K.; Pothier, Joël F.; Zézé, Adolphe; Perret, Xavier,

2020.

Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d’Ivoire.

International Journal of Systematic and Evolutionary Microbiology.

70(2),

pp.1421-1430.

Available from: https://doi.org/10.1099/ijsem.0.003931

Oh, Woo Taek; Jun, Jin Woo; Giri, Sib Sankar; Yun, Saekil; Kim, Hyoun Joong; Kim, Sang Guen; Kim, Sang Wha; Kang, Jeong Woo; Han, Se Jin; Kwon, Jun; Kim, Ji Hyung; Smits, Theo H.M.; Park, Se Chang,