Thursday, April 24, 2025
COST Action MiCropBiomes CA22158

Resources

Documents for Download:

Bodies, Consortia and Useful Websites:

  • MiCropBiomes LinkedIn Account
  • MiCropBiomes X (ex-Twitter) Account
  • CABI: Centre for Agriculture and Bioscience International
  • COST: European CoOperation in Science and Technology
  • EFSA: European Food Safety Authority
  • EPPO: European and Mediterranean Plant Protection Organisation
  • Euphresco: Network of organisations funding research projects and coordinating national research in the phytosanitary area
  • Phytobiomes Alliance: An industry-academic collaborative initiative focused on building a phytobiome-based foundation for accelerating the sustainable production of food, feed, and fiber.
  • ROOT-BENEFIT: COST Action CA22142 on “Beneficial root-associated microorganisms for sustainable agriculture”
  • BIOVEXO: Biocontrol of Xylella and its vector in olive trees for integrated pest management
  • DROP: XF-ACTORS Digital Research Object Portal
  • Database of host plants found to be susceptible to Xylella fastidiosa in the European Union territory
  • DokuWiki: A Xanthomonas Wiki resource about molecular diagnosis and diversity, type III effectors and plant resistance genes

MiCropBiomes Newsletters:

  • Newsletter no. 1 – Welcome! (February 15, 2024)
  • Newsletter no. 2 – Website & Newsletter (February 23, 2024)
  • Newsletter no. 3 – Short Term Scientific Missions (February 27, 2024)
  • Newsletter no. 4 – Social Media (April 2, 2024)
  • Newsletter no. 5 – Short-Term Scientific Missions (May 22, 2024)
  • Newsletter no. 6 – First Annual Conference (May 27, 2024)
  • Newsletter no. 7 – First Training School (June 14, 2024)
  • Newsletter no. 8 – First Annual Conference – Confirmed Speakers (August 12, 2024)
  • Newsletter no. 9 – Collaborative Glossary Initiative (September 2, 2024)
  • Newsletter no. 10 – Third STSM Call (September 18, 2024)
  • Newsletter no. 11 – First Annual Conference – Book of Abstracts (September 30, 2024)
  • Newsletter no. 12 – Happy New Year! (January 3, 2025)
  • Newsletter no. 13 – Short-Term Scientific Missions in 2025 (February 10, 2025)
  • Newsletter no. 14 – Upcoming Conferences (March 6, 2025)
  • Newsletter no. 15 – Second Annual Conference (April 1, 2025)
  • Newsletter no. 16 – Second Training School (April 10, 2025)
  • Newsletter no. 17 – Fourth STSM Call (April 15, 2025)

Important Groups of Plant Pathogens (BSPP):

  • The Top 10 plant pathogenic bacteria in molecular plant pathology, incl. Agrobacterium tumefaciens, Dickeya (dadantii and solani), Erwinia amylovora, Pectobacterium (atrosepticum and carotovorum), Pseudomonas syringae, Ralstonia solanacearum, Xanthomonas spp. and Xylella fastidiosa
  • The Top 10 fungal pathogens in molecular plant pathology, incl. Blumeria graminis, Botrytis cinerea, Colletotrichum spp., Fusarium (graminearum and oxysporum), Magnaporthe oryzae, Melampsora lini, Mycosphaerella graminicola, Puccinia spp. and Ustilago maydis
  • The Top 10 oomycete pathogens in molecular plant pathology, incl. Albugo candida, Hyaloperonospora arabidopsidis, Pythium ultimum, Phytophthora (capsici, cinnamomi, infestans, parasitica, ramorum, sojae), Plasmopara viticola
  • Top 10 plant viruses in molecular plant pathology, incl. African cassava mosaic virus (ACMV), Brome mosaic virus (BMV), Cauliflower mosaic virus (CaMV), Cucumber mosaic virus (CMV), Plum pox virus (PPV), Potato virus X (PVX), Potato virus Y (PVY), Tobacco mosaic virus (TMV), Tomato spotted wilt virus (TSWV), Tomato yellow leaf curl virus (TYLCV)
  • Top 10 plant-parasitic nematodes in molecular plant pathology, incl. Aphelenchoides besseyi, Bursaphelenchus xylophilus, Ditylenchus dipsaci, Heterodera and Globodera spp., Meloidogyne spp., Nacobbus aberrans, Pratylenchus spp., Radopholus similis, Rotylenchulus reniformis, Xiphinema index
  • Not in your usual Top 10: Protists that infect plants and algae, incl. Eurychasma dicksonii, Labyrinthula spp., Olpidiopsis spp., Pythium porphyrae, Phytomonas spp., Plasmodiophora brassicae, Polymyxa spp., Spongospora subterranea

Relevant Publications:

  • Beattie GA, Bayliss KL, Jacobson DA, Broglie R, Burkett-Cadena M, Sessitsch A, Kankanala P, Stein J, Eversole K, Lichens-Park A (2024). From microbes to microbiomes: applications for plant health and sustainable agriculture. Phytopathology 114: 1742-1752. doi: 10.1094/PHYTO-02-24-0054-KC
  • Berg G, Rybakova D, Fischer D, Cernava T, Vergès MC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran GS, Selvin J, Souza RSC, van Overbeek L, Singh BK, Wagner M, Walsh A, Sessitsch A, Schloter M (2020). Microbiome definition re-visited: old concepts and new challenges. Microbiome 8: 103. doi: 10.1186/s40168-020-00875-0
  • Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt W-D, Hatzimanikatis V, Heiman CM, Herzog MK-M, Hockenberry A, Keel C, Keppler A, Lee S-J, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh H-J, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA (2023). From microbiome composition to functional engineering, one step at a time. Microbiol. Mol. Biol. Rev. 87: e0006323. doi: 10.1128/mmbr.00063-23
  • Cheng YT, Zhang L, He SY (2019). Plant-microbe interactions facing environmental challenge. Cell Host Microbe 26: 183-192. doi: 10.1016/j.chom.2019.07.009
  • Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, Sessitsch A (2025). Harnessing the plant microbiome for sustainable crop production. Nat. Rev. Microbiol. 23: 9-23. doi: 10.1038/s41579-024-01079-1
  • Dastogeer KM, Tumpa FH, Sultana A, Akter MA, Chakraborty A (2020). Plant microbiome – an account of the factors that shape community composition and diversity. Curr. Plant Biol. 23: 100161. doi: 10.1016/j.cpb.2020.100161
  • Deng S, Meier MA, Caddell D, Yang J, Coleman-Derr D (2022). Plant microbiome-based genome-wide association studies. Methods Mol. Biol. 2481: 353-367. doi: 10.1007/978-1-0716-2237-7_20
  • Ellis JG (2017). Can plant microbiome studies lead to effective biocontrol of plant diseases? Mol. Plant Microbe Interact. 30: 190-193. doi: 10.1094/MPMI-12-16-0252-CR
  • Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL (2020). The plant microbiome: from ecology to reductionism and beyond. Annu. Rev. Microbiol. 74: 81-100. doi: 10.1146/annurev-micro-022620-014327
  • Gutierrez A, Grillo MA (2022). Effects of domestication on plant-microbiome interactions. Plant Cell Physiol. 63: 1654-1666. doi: 10.1093/pcp/pcac108
  • Hacquard S, Wang E, Slater H, Martin F (2022). Impact of global change on the plant microbiome. New Phytol. 234: 1907-1909. doi: 10.1111/nph.18187
  • Jian Y, Gong D, Wang Z, Liu L, He J, Han X, Tsuda K (2024). How plants manage pathogen infection. EMBO Rep. 25: 31-44. doi: 10.1038/s44319-023-00023-3
  • Leach JE, Triplett LR, Argueso CT, Trivedi P (2017). Communication in the phytobiome. Cell 169: 587-596. doi: 10.1016/j.cell.2017.04.025
  • Klassen JL (2018). Defining microbiome function. Nat. Microbiol. 3: 864-869. doi: 10.1038/s41564-018-0189-4
  • Li P, Dini-Andreote F, Jiang J (2024). Exploiting microbial competition to promote plant health. Trends Plant Sci. 29: 1056-1058. doi: 10.1016/j.tplants.2024.05.003
  • Liu X, Cai J, Li X, Yu F, Wu D (2022). Can bacterial type III effectors mediate pathogen-plant-microbiota ternary interactions? Plant Cell Environ. 45: 5-11. 10.1111/pce.14185
  • Marchesi JR, Ravel J (2015). The vocabulary of microbiome research: a proposal. Microbiome 3: 31. doi: 10.1186/s40168-015-0094-5
  • Martins SJ, Pasche J, Silva HAO, Selten G, Savastano N, Abreu LM, Bais HP, Garrett KA, Kraisitudomsook N, Pieterse CMJ, Cernava T (2023). The use of synthetic microbial communities to improve plant health. Phytopathology 113: 1369-1379. doi: 10.1094/PHYTO-01-23-0016-IA
  • Müller DB, Vogel C, Bai Y, Vorholt JA (2016). The plant microbiota: systems-level insights and perspectives. Annu. Rev. Genet. 50: 211-234. doi: 10.1146/annurev-genet-120215-034952
  • Orozco-Mosqueda MDC, Rocha-Granados MDC, Glick BR, Santoyo G (2018). Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol. Res. 208: 25-31. doi: 10.1016/j.micres.2018.01.005
  • Pacheco AR, Vorholt JA (2023). Resolving metabolic interaction mechanisms in plant microbiomes. Curr. Opin. Microbiol. 74: 102317. doi: 10.1016/j.mib.2023.102317
  • Pantigoso HA, Newberger D, Vivanco JM (2022). The rhizosphere microbiome: plant-microbial interactions for resource acquisition. J. Appl. Microbiol. 133: 2864-2876. doi: 10.1111/jam.15686
  • Rangel LI, Leveau JHJ (2024). Applied microbiology of the phyllosphere. Appl. Microbiol. Biotechnol. 108: 211. doi: 10.1007/s00253-024-13042-4
  • Sohrabi R, Paasch BC, Liber JA, He SY (2023). Phyllosphere microbiome. Annu. Rev. Plant Biol. 74: 539-568. doi: 10.1146/annurev-arplant-102820-032704
  • Song S, Liu Y, Wang NR, Haney CH (2021). Mechanisms in plant-microbiome interactions: lessons from model systems. Curr. Opin. Plant Biol. 62: 102003. doi: 10.1016/j.pbi.2021.102003
  • Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK (2020). Plant-microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18: 607-621. doi: 10.1038/s41579-020-0412-1
  • Turner TR, James EK, Poole PS (2013). The plant microbiome. Genome Biol. 14: 209. doi: 10.1186/gb-2013-14-6-209
  • Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015). The importance of the microbiome of the plant holobiont. New Phytol. 206: 1196-206. doi: 10.1111/nph.13312
  • Vayssier-Taussat M, Albina E, Citti C, Cosson JF, Jacques MA, Lebrun MH, Le Loir Y, Ogliastro M, Petit MA, Roumagnac P, Candresse T (2014). Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Front. Cell. Infect. Microbiol. 4: 29. doi: 10.3389/fcimb.2014.00029
  • Vorholt JA, Vogel C, Carlström CI, Müller DB (2017). Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22: 142-155. doi: 10.1016/j.chom.2017.07.004
  • Willis AD, Clausen DS (2025). Planning and describing a microbiome data analysis. Nat. Microbiol, in press. doi: 10.1038/s41564-025-01944-6
  • Xu X, Dinesen C, Pioppi A, Kovács ÁT, Lozano-Andrade CN (2025). Composing a microbial symphony: synthetic communities for promoting plant growth. Trends Microbiol., in press. doi: 10.1016/j.tim.2025.01.006
  • Xu L, Pierroz G, Wipf HM, Gao C, Taylor JW, Lemaux PG, Coleman-Derr D (2021). Holo-omics for deciphering plant-microbiome interactions. Microbiome 9: 69. doi: 10.1186/s40168-021-01014-z