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5. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Author

Alvarez-Ordóñez, Avelino, Alvarez, Pablo, Antonielli, Livio, Arendt, Elke, Armanini, Federica, Aubry, Aurelie, Baelum, Jacob, Barcenilla, Coral, Belanche, Alejandro, Benavent-Gil, Yaiza, Blake, Tony, Blanco-Míguez, Aitor, Bongoni, Radhika, Boyer, Mickael, Brennan, Fiona, Breselge, Samuel, Briem, Helgi, Butler, Derek, Calvete-Torre, Inés, Carballo, Omar Cristobal, Cardinal, Mireille, Carlino, Niccolò, Chervaux, Christian, Chopin, Christine, Clotaire, Natallia, Coakley, Mairead, Cobo-Díaz, José Francisco, Codd, Jim, Conroy, Stephen, Corral-Jara, Karla Fabiola, Corral-Jara, Karla-Fabiola, Cotter, Paul D., Coyne, Gerard, Creevey, Chris, Cuevas, Patricia D., Curran, Brendan, Delgado, Susana, Derde, Liesbeth, Derrien, Muriel, Ercolini, Danilo, Exposito, Ruth Gomez, López Fernández, María Mercedes, De Filippis, Francesca, Fordham, Daniel, Galy, Hubert, Gavriilidou, Asimenia, Gunnarsson, Oddur, Hanson, Buck, Hermes, Gerben, Huang, Rongcai, Huws, Sharon, Ikoyi, Israel, Jaeger, Alice, Jeffery, Ian, Jérôme, Marc, Juan, Pierre-Alexandre, Kenny, David, Kers, Annelies, Khinouche, Karim-Franck, Kirwan, Stuart, Klaassens, Eline S., Knobloch, Stephen, Kolbeinsson, Kristinn, Kolypczuk, Laetitia, Kostic, Tanja, Ledda, Fabio, Leech, John, Lehmann, Doerte, Leroi, Françoise, Lewis, Eva, Ley, Johanna, Lucic, Eva, Lynch, Kieran, Mace, Sabrina, MacLaren-Lee, Iain, Mahler de Sanchez, Lisa, Marchart, Juergen, Margolles, Abelardo, Marteinsson, Viggó Thór, Masetti, Giulia, McGovern, Fiona, McHugh, Noirin, McLoughlin, Steven, Meehan, Dara, Mølbak, Lars, Monin, Thomas, Moreno, Javier, Morgavi, Diego, Morrison, Steven, Müench, Steffen, Ramos Neves, Ana Rute, Neylon, Emma, Nyhan, Laura, O’Kelly, Rhona, O’Neil, Dominic, O’Toole, Paul, Ortiz-Chura, Abimael, Palma, Juan Manuel, Pasolli, Edoardo, Passerini, Delphine, Pastar, Milica, Pinto, Federica, Pirovano, Walter, Plans, Olga, Policht, Marion, Pop, Aurel, Pop, Bianca, Popova, Milka, Prieto, Miguel, Quijada, Narciso M., Reiss, Antje, Romero, Pedro, Ruas-Madiedo, Patricia, Rubino, Francesco, Rubio, Raul Cabrera, Ruiz, Lorena, Ryan, Angela, Ryan, Clodagh, Sabater, Carlos, Sahin, Aylin, Salaun, Cecile, Santos, Fernanda Godoy, Schneider, Carolin, Segata, Nicola, Selberherr, Evelyne, Sessitsch, Angela, Skírnisdóttir, Sigurlaug, Smidt, Hauke, Smith, Paul, Sprenger-Haussels, Markus, Tapio, Ilma, Tap, Julien, Valentino, Vincenzo, Wagner, Martin, Walsh, Aaron, Walsh, Liam, Waters, Sinead M., Willcocks, Spike, Yáñez-Ruiz, David R., Yan, Tianhai, Yap, Min, Zannini, Emanuele, Zuliani, Véronique, Punčochář, Michal, Mengoni, Claudia, Tatti, Alessia, Manghi, Paolo, Avagliano, Michele, Cabrera-Rubio, Raul, Coakley, Mairéad, Cobo-Díaz, José F., Dey, Hrituraj, Asnicar, Francesco, Fackelmann, Gloria, Heidrich, Vitor, and Rota Stabelli, Omar

Published
2024
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11. Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea

Author

Benucci, Gian Maria Niccolò, Haridas, Sajeet, Labutti, Kurt, Marozzi, Giorgio, Antonielli, Livio, Sanchez, Sergio, Marco, Pedro, Wang, Xinxin, Barry, Kerrie, Lipzen, Anna, Chovatia, Mansi, Hundley, Hope, Falini, Leonardo Baciarelli, Murat, Claude, Martin, Francis, Albertini, Emidio, Donnini, Domizia, Grigoriev, Igor V, and Bonito, Gregory

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Human Genome, Biochemistry and Cell Biology
Abstract

Sphaerosporella brunnea is a pioneer ectomycorrhizal fungus with facultative saprophytic capacities. Here, we sequenced the genome of S. brunnea strain Sb_GMNB300, which is estimated at 51.6 Mb in size with 872 assembled contigs accounting for 12,597 predicted coding genes. This genome will be useful for comparative studies of Pezizales ectomycorrhizal symbioses.

Published
2019

18. Microbial Fermentation and Shelf Life of Potential Biotechnological Products Capable of Pesticide Degradation.

Author

Kraxberger, Katharina, Kostić, Tanja, Antonielli, Livio, and Sessitsch, Angela

Subjects
BIOTECHNOLOGY, MICROBIAL products, BACILLUS subtilis, COMMERCIAL product testing, ORGANIC acids, MICROBIAL inoculants
Abstract

The pesticide active ingredient azoxystrobin is widely used in agriculture and has negative effects for the environment and contained organisms. Bacterial strains have been reported to degrade azoxystrobin, but precise methodologies for producing and storing these strains as potential biotechnological products are lacking. The study focused on creating and optimising a non-sterile, small-scale microbial fermentation protocol to produce azoxystrobin-degrading products and to test their shelf life. By testing 14 variants and sampling at three production and two storage time points, the trial demonstrated the successful production and storage of microbial products capable of pesticide degradation. Various measurement parameters such as pH value and organic acids were used to monitor the quality of the microbial products during the production and storage. Further, we developed and validated qPCR assays to rapidly and specifically assess the concentration of the two azoxystrobin degrading strains, namely Bacillus subtilis strain MK101 and Rhodococcus fascians strain MK144. To ensure good specificity, the combination of two qPCR assays targeting two different genome regions was implemented for each strain. The study highlights the significant impact of media selection and bacterial inoculum quantity on the microbial product quality. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats.

Author

Csorba, Cintia, Rodić, Nebojša, Antonielli, Livio, Sessitsch, Angela, Vlachou, Angeliki, Ahmad, Muhammad, Compant, Stéphane, Puschenreiter, Markus, Molin, Eva M., Assimopoulou, Andreana N., and Brader, Günter

Subjects
SOIL acidity, MICROBIAL diversity, ACID soils, PLANT genetics, METABOLOMICS
Abstract

Improved understanding of the complex interaction between plant metabolism, environmental conditions and the plant-associated microbiome requires an interdisciplinary approach: Our hypothesis in our multiomics study posited that several environmental and biotic factors have modulating effects on the microbiome and metabolome of the roots of wild Echium vulgare plants. Furthermore, we postulated reciprocal interactions between the root metabolome and microbiome. We investigated the metabolic content, the genetic variability, and the prokaryotic microbiome in the root systems of wild E. vulgare plants at rosette and flowering stages across six distinct locations. We incorporated the assessment of soil microbiomes and the measurement of selected soil chemical composition factors. Two distinct genetic clusters were determined based on microsatellite analysis without a consistent alignment with the geographical proximity between the locations. The microbial diversity of both the roots of E. vulgare and the surrounding bulk soil exhibited significant divergence across locations, varying soil pH characteristics, and within the identified plant genetic clusters. Notably, acidophilic bacteria were characteristic inhabitants of both soil and roots under acidic soil conditions, emphasizing the close interconnectedness between these compartments. The metabolome of E. vulgare significantly differed between root samples from different developmental stages, geographical locations, and soil pH levels. The developmental stage was the dominant driver of metabolome changes, with significantly higher concentrations of sugars, pyrrolizidine alkaloids, and some of their precursors in rosette stage plant roots. Our study featured the complex dynamics between soil pH, plant development, geographical locations, plant genetics, plant metabolome and microbiome, shedding light on existing knowledge gaps. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Dimensiones del conflicto: resistencia, violencia y policía en el mundo urbano

Author

Aguirre, Susana Elsa, additional, Abián Cubillo, David A., additional, Álvarez Delgado, Lorena, additional, Antonielli, Livio, additional, F. Armesto, Mónica, additional, Bonnefoy, Baptiste, additional, Busquest Alemany, Anna, additional, Castro Redondo, Rubén, additional, Cebreiro Ares, Francisco, additional, De Benedictis, Angela, additional, Fernández Flórez, Marina, additional, Llanes Parra, Blanca, additional, Lopes, Maria Antónia, additional, Mantecón Movellán, Tomás Antonio, additional, Martín Marcos, David, additional, Pereyra, Osvaldo Víctor, additional, Polo Sánchez, Julio Juan, additional, Sagredo Baeza, Rafael, additional, Serna Vallejo, Margarita, additional, Sixto Barcia, Ana María, additional, Torres Arce, Marina, additional, Truchuelo García, Susana, additional, Velasco Tejedor, Rocío, additional, Díaz Ceballos, Jorge, additional, and Torres Trimállez, Marina, additional

Published
2020
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33. Taxonomic and functional analysis of the endophytic microbiome associated with wild cold-adapted Rosaceae plants

Author

Marian, Malek, Milanese, Irma, Antonielli, Livio, and Perazzolli, Michele

Subjects
Plant Microbiome, Alpine Region, Cold Stress, Rosaceae Plants, Psychrotolerant Bacteria, Plant Growth Promotion
Abstract

Climate change-associated extreme weather events such as early spring frosts have increased in frequency and intensity over the past decades. Cold stress is one of the main limiting factors for fruit crop production worldwide. Plants growing in cold regions, such as alpine regions, are hypothesized to survive cold stress thanks to symbiosis with endophytic microorganisms. However, the structure and function of endophytic microbial communities associated with such plants are poorly understood. Here, we collected three wild cold-adapted Rosaceae plants (Geum montanum, Alchemilla sp. and Dryas octopetala) from seven different sites in Italy from two expositions (North and South). Using 16S rRNA gene amplicon sequencing, we characterized the bacterial community structure across three compartments (flowers, leaves and roots) to identify potential candidate taxa for cold tolerance. We complemented this analysis with a culture-dependent approach, a combination of a low nutrient medium (Reasoner's 2A agar), long incubation time (up to 4 weeks) and low temperature (at 4°C), to recover culturable psychrotolerant bacterial taxa. We successfully established a taxonomically diverse bacterial culture collections representing the majority of dominant genera detectable by culture-independent community profiling, including Pseudomonas, Erwinia, Sphingomonas, Rhizobium, Massilia, Janthinobacterium, Duganella and Flavobacterium. Additional work will test these isolates for their cold stress alleviation capacities on tomato and apple. Understanding the role of microbiomes in cold stress tolerance of plants will help to develop relevant bacterial inoculants for agricultural systems.

Published
2022
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34. Exploring the functional potential of plant-associated microbiomes in alpine region to enhance cold stress tolerance in plants

Author

Marian, Malek, Milanese, Irma, Antonielli, Livio, and Perazzolli, Michele

Subjects
Plant Microbiome, Alpine Region, Cold Stress, Rosaceae Plants, Psychrotolerant Bacteria, Plant Growth Promotion
Abstract

Climate change-associated extreme weather events such as early spring frosts have increased in frequency and intensity over the past decades. Cold stress is one of the main limiting factors for fruit crop production worldwide. Plants and their associated microbial communities have developed complex adaptation strategies against cold stress. Plants growing in cold regions, such as alpine regions, are hypothesized to survive cold stress thanks to symbiosis with endophytic microorganisms. However, the structure and function of endophytic microbial communities associated with such plants are poorly understood. Our aim is to taxonomically and functionally characterize the endophytic bacterial communities associated with three wild cold-adapted Rosaceae plants (i.e.Geum montanum, Alchemilla sp., and Dryas octopetala) from alpine region. Plant samples were collected from seven different sites in Italy from two expositions (North and South). The bacterial community structure associated with the flowers, leaves, and roots were characterized using 16S rRNA gene (V5–V7region) amplicon sequencing to identify potential candidate taxa for cold tolerance. In addition, targeted isolation methods were used to recover culturable psychrotolerant bacterial taxa through a combination of a low nutrient medium (Reasoner's 2A agar), long incubation time (up to 4 weeks) and low temperature (at 4°C). Plant species,tissues, and sites were the main factors influencing bacterial richness, diversity,and community structure. Furthermore, we established a taxonomically diverse psychrotolerant bacterial culture collections (about 700 isolates belonging to 54 different genera) representing the majority of dominant genera detectable by culture-independent community profiling, including Pseudomonas, Erwinia, Sphingomonas, Rhizobium, Massilia, Janthinobacterium, Duganella, Flavobacterium, Mucilaginibacter, Subtercola, and Galbitalea. This study contributes to the understanding of plant-associated microbiomes in alpine regions, and highlight their potential as bioinoculants for the enhancement of cold stress tolerance in agronomically relevant fruit crops.

Published
2022
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35. Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines

Author

Darriaut, Romain, primary, Antonielli, Livio, additional, Martins, Guilherme, additional, Ballestra, Patricia, additional, Vivin, Philippe, additional, Marguerit, Elisa, additional, Mitter, Birgit, additional, Masneuf-Pomarède, Isabelle, additional, Compant, Stéphane, additional, Ollat, Nathalie, additional, and Lauvergeat, Virginie, additional

Published
2022
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36. Metabolite Production in Alkanna tinctoria Links Plant Development with the Recruitment of Individual Members of Microbiome Thriving at the Root-Soil Interface

Author

Csorba, Cintia, primary, Rodić, Nebojša, additional, Zhao, Yanyan, additional, Antonielli, Livio, additional, Brader, Günter, additional, Vlachou, Angeliki, additional, Tsiokanos, Evangelia, additional, Lalaymia, Ismahen, additional, Declerck, Stéphane, additional, Papageorgiou, Vassilios P., additional, Assimopoulou, Andreana N., additional, and Sessitsch, Angela, additional

Published
2022
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38. Deciphering the anthosphere and endosphere microbiome of wild Rosaceae plants for cold-adapted plant growth promoting bacteria

Author

Marian Malek, Milanese Irma, Antonielli Livio, Pertot Ilaria, and Perazzolli Michele

Subjects
food and beverages, Plant Microbiome, Alpine Region, Cold Stress, Rosaceae Plants, Psychrotolerant Bacteria, Plant Growth Promotion
Abstract

Cold stress is one of the main limiting factors for fruit crop production worldwide. Plants and their associated microbial communities have developed complex adaptation strategies against different abiotic stresses, cold stress included. Plants growing in cold regions, such as alpine and sub-alpine regions, are hypothesized to survive cold stress thanks to symbiosis with endophytic microorganisms. However, the structure and function of endophytic microbial communities associated with such plants are poorly understood. Our aim is to taxonomically and functionally characterize the endophytic bacterial communities associated with three wild cold-adapted Rosaceae plants (i.e. Geum montanum, Alchemilla sp., and Dryas octopetala) from alpine region. Plant samples were collected from seven different sites in Italy from two expositions (North and South). The bacterial community structure associated with the flowers, leaves, and roots were characterized using 16S rRNA gene (V5–V7region) amplicon sequencing to identify potential candidate taxa for cold tolerance. In addition, targeted isolation methods were used to recover culturable psychrotolerant bacterial taxa through a combination of a low nutrient medium (Reasoner's 2A agar), long incubation time (up to 4 weeks) and low temperature (at 4°C). Data generated through this work increase our understanding of the structure and function of the microbiome of wild Rosaceae plants, which may allow the design of efficient bacterial inoculants for enhancing cold stress tolerance in agronomically relevant fruit crops. The project has received funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska Curie grant agreement number 101021787 (project FreezingBioprotector).

Published
2022
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39. Metabolite Production in Alkanna tinctoria Links Plant Development with the Recruitment of Individual Members of Microbiome Thriving at the Root-Soil Interface

Author

UCL - SST/ELI - Earth and Life Institute, Csorba, Cintia, Rodić, Nebojša, Zhao, Yanyan, Antonielli, Livio, Brader, Günter, Vlachou, Angeliki, Tsiokanos, Evangelia, Lalaymia, Ismahen, Declerck, Stéphane, Papageorgiou, Vassilios P., Assimopoulou, Andreana N., Sessitsch, Angela, Bulgarelli, Davide, UCL - SST/ELI - Earth and Life Institute, Csorba, Cintia, Rodić, Nebojša, Zhao, Yanyan, Antonielli, Livio, Brader, Günter, Vlachou, Angeliki, Tsiokanos, Evangelia, Lalaymia, Ismahen, Declerck, Stéphane, Papageorgiou, Vassilios P., Assimopoulou, Andreana N., Sessitsch, Angela, and Bulgarelli, Davide

Abstract

Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used enantiomers alkannin and shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms, we performed a greenhouse experiment in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages, we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all extracted primary and secondary metabolite content of root material. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin derivatives at the fruiting stage. Plant root microbial diversity was influenced both by bulk soil origin and to a small extent by the developmental stage. The performed correlation analyses and cooccurrence networks on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic and at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial genera Labrys and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium as well as four species of the fungal genus Penicillium were found to be positively correlated with higher content of alkannins. IMPORTANCE Previous studies have shown that individual, isolated microorganisms may influence secondary metabolism of plants and induce or stimulate the production of medicinally relevant secondary metabolism. Here, we analyzed the microbiome-metabolome linkage of the medicinal plant Alkanna tinctoria, which is kn

Published
2022

45. Lombardie et Pays-Bas autrichiens

Author

Antoine, François, Bernard, Bruno, Galand, Michèle, Antonielli, Livio, Heirwegh, Jean-Jacques, Brambilla, Elena, Bruneel, Claude, Capra, Carlo, Denys, Catherine, di Renzo Villata, Gigliola, Legay, Marie-Laure, Vitali-Volant, Maria Giuseppina, and Logie, Jacques

Subjects
History, bic Book Industry Communication::H Humanities::HB History
Abstract

Au cours de la seconde moitié du XVIIIe siècle, la monarchie habsbourgeoise entama des réformes visant à modifier une série de paramètres de la vie politique et sociale, d’abord, le plus souvent, dans ses possessions italiennes, dont la Lombardie était la plus vaste, puis dans les Pays-Bas. Dans ce volume, une douzaine d’historiens universitaires, belges, français et italiens, se livrent à un vaste tour d’horizon de ces réformes, des conditions de leur mise en œuvre et de la réception qu’elles ont reçue dans ces deux territoires, alors également soumis aux autorités politiques viennoises, mais disposant chacun, cependant, d’une certaine autonomie au sein de la monarchie habsbourgeoise. Tour à tour toutes les grandes questions de l’époque sont abordées, depuis les relations de ces provinces avec Vienne jusqu’aux tentatives de modernisation de l’enseignement, de la police ou de la justice, en passant par les rapports tendus qu’entretenaient, en Lombardie et dans les Pays-Bas, l’Église et l’État, les réformes économiques mises en œuvre dans ces deux provinces, ou encore les solutions qu’on tenta d’y apporter aux difficiles questions de l’assistance aux pauvres et de la santé. Tous les textes de ce volume sont pourvus d’un bref résumé en italien.

Published
2008

47. Bacteria associated with wood tissues of Esca‐diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components

Author

Haidar, Rana, primary, Yacoub, Amira, additional, Vallance, Jessica, additional, Compant, Stéphane, additional, Antonielli, Livio, additional, Saad, Ahmad, additional, Habenstein, Birgit, additional, Kauffmann, Brice, additional, Grélard, Axelle, additional, Loquet, Antoine, additional, Attard, Eléonore, additional, Guyoneaud, Rémy, additional, and Rey, Patrice, additional

Published
2021
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48. Potato Root-Associated Microbiomes Adapt to Combined Water and Nutrient Limitation and have a Plant Genotype-Specific Role for Plant Stress Mitigation

Author

Faist, Hanna, Trognitz, Friederike, Antonielli, Livio, Symanczik, Sarah, White, Philip, Sessitsch, Angela, Faist, Hanna, Trognitz, Friederike, Antonielli, Livio, Symanczik, Sarah, White, Philip, and Sessitsch, Angela

Abstract

Background Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a eld experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure.

Published
2021

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