Legume tasters: symbiotic rhizobia host preference and smart inoculant formulations

Mutualistic interactions have great importance in ecology, with genetic information that takes shape through interactions within the symbiotic partners and between the partners and the environment. It is known that variation of the host-associated microbiome contributes to buffer adaptation challenges of the host’s physiology when facing varying environmental conditions. In agriculture, pivotal examples are symbiotic nitrogen-fixing rhizobia, known to contribute greatly to host (legume plants) adaptation and host productivity. A holistic view of increasing crop yield and resistance to biotic and abiotic stresses is that of microbiome engineering, the exploitation of a host-associated microbiome through its rationally designed manipulation with synthetic microbial communities. However, several studies highlighted that the expression of the desired phenotype in the host resides in species-specific, even genotype-specific interactions between the symbiotic partners. Consequently, there is a need to dissect such an intimate level of interaction, aiming to identify the main genetic components in both partners playing a role in symbiotic differences/host preferences. In the present paper, while briefly reviewing the knowledge and the challenges in plant–microbe interaction and rhizobial studies, we aim to promote research on genotype x genotype interaction between rhizobia and host plants for a rational design of synthetic symbiotic nitrogen-fixing microbial communities to be used for sustainably improving leguminous plants yield.This work was supported by the grant MICRO4Legumes (“Il microbioma vegetale simbionte come strumento per il miglioramento delle leguminose foraggere. Acronimo”), D.M.n.89267 (Italian Ministry of Agriculture)

The green deal challenge: exploiting biotic interactions from bacterial strains to communities

One of the main factors behind agricultural sustainability is the effective management of nitrogen (N) inputs, a key element for crop production. Plant growth and agricultural yield is a result of complex interactions between the plant, soil and its microbial communities. An effective way for the management of N inputs resulting in farming practices that are economically viable and environmentally prudent is the use of biologically fixed nitrogen. Symbiotic nitrogen fixing bacteria (rhizobia) represent a promising source of biologically fixed nitrogen, since they provide N inputs directly into the plant (legume). The overarching aim of this thesis is the description, the deciphering and exploitation of the microbial contribution to environmental sustainability. The first chapter of this thesis focuses on the above-mentioned topic, the symbiosis between legumes and rhizobia, ranging from the most recent discoveries on rhizobia to improve agricultural practices in harsh soils to the choice of the best partnership. Although being species-specific, rhizobia in nature exhibit somewhat large variation in the symbiotic efficiency with different varieties of the same host plant species, which may limit their application to crop as inoculants. While the molecular basis for the species-specificity have been well defined, the molecular basis of the specificity between the variety plant and the bacterial strains belonging to the same species are unknown. In this chapter, the evolutions of the partnership along the genus and its pangenome is dissected and the model species for plant-rhizobium symbiosis, Sinorhizobium meliloti (syn. Ensifer) and Medicago sativa (alfalfa) became our model to investigate the host-symbiont recognition during the initial perception. Next to the novel findings on the evolution of symbiotic nitrogen fixation in the genus, taxonomic revision of the Sinorhizobium/Ensifer genus as well indicates some guidelines for genus delineation in Rhizobiaceae. The second chapter focuses on the study of the microbiota and its interaction with the environment, analysing the signatures of microbial life in nature. Environmental microbiology can be defined as the study of microbes, their functions, and interactions in all habitats on Earth (and beyond). The papers presented in this chapter are aimed at exploring three different environments sharing the feature of being “extreme”, that is non-conventional for aerobic, mesophilic microbes. The third chapter reports a systems-biology investigation of metabolic adaptation strategies with a study on the diauxie, showing the metabolic networks of Pseudoalteromonas haloplanktis (a heterotrophic marine bacterium) in complex nutritional conditions encountered in the environment.Uno dei principali fattori alla base della sostenibilità ambientale è la gestione efficace degli input di azoto (N), un elemento chiave per la produzione agricola. La crescita delle piante e la resa agricola sono il risultato di complesse interazioni tra la pianta, il suolo e le sue comunità microbiche. Un modo efficace per la gestione degli input di azoto, che ha come risultato lo sviluppo di pratiche agricole economicamente valide e rispettose dell'ambiente, è l'uso di azoto fissato biologicamente. I batteri simbionti azoto fissatori (rizobi) rappresentano una preziosa fonte di azoto fissato biologicamente, poiché forniscono alla pianta (legume) questo importante elemento direttamente a livello della radice. Il primo capitolo di questa tesi si concentra sull'argomento appena menzionato, la simbiosi tra piante leguminose e rizobi, spaziando dalle più recenti scoperte sui rizobi, volte a migliorare le pratiche agricole in terreni di difficile coltivazione, alla scelta del miglior partenariato. Sebbene siano specie-specifici, i rizobi in natura mostrano una variabilità piuttosto ampia nell'efficienza simbiotica con diverse varietà della stessa specie di pianta ospite, il che può limitare la loro applicazione come inoculanti per le colture. Mentre le basi molecolari della specie-specificità sono state ben definite, quelle che determinano la specificità tra la varietà vegetale e ceppi batterici appartenenti alla stessa specie sono sconosciute. In questo primo capitolo, vengono sezionate le evoluzioni della partnership simbiotica fra pianta e rizobio. Le specie modello Sinorhizobium meliloti (syn. Ensifer) e Medicago sativa (erba medica) sono diventate il nostro modello per studiare il riconoscimento ospite-simbionte durante la percezione reciproca iniziale. Accanto alle nuove scoperte sull'evoluzione della fissazione dell'azoto simbiotico, la revisione tassonomica del genere Sinorhizobium/Ensifer indica alcune linee guida per la delineazione del genere nelle Rhizobiaceae. Il secondo capitolo si concentra sullo studio del microbiota e della sua interazione con l'ambiente, analizzando le “firme” della vita microbica in natura. La microbiologia ambientale può essere definita come lo studio dei microrganismi, delle loro funzioni e interazioni in tutti gli habitat della Terra (e oltre). Gli articoli presentati in questo capitolo hanno lo scopo di esplorare tre diversi ambienti che condividono la caratteristica di essere “estremi”, non convenzionali, per i microbi aerobici, mesofili. Il terzo capitolo riporta un'indagine di biologia dei sistemi delle strategie di adattamento metabolico con uno studio sulla diauxia, che mostra le reti metaboliche di Pseudoalteromonas haloplanktis (un batterio marino eterotrofico) in complesse condizioni nutrizionali incontrate nell'ambiente

A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists

Making use of mathematics and statistics, bioinformatics helps biologists to quickly obtain information from a huge amount of experimental data. Nowadays, a large number of web- and computer-based tools are available, allowing more unskilled scientists to be familiar with data analysis techniques. The present chapter gives an overview of the most easy-to-use tools and software packages for bacterial genes and genome analysis present on the Web, with the aim to mainly help wet-lab researcher at undergraduate and postgraduate levels to introduce them to bioinformatics analysis of biological data

Endophytes: Improving Plant Performance

Endophytes represent microorganisms that reside within plant tissues, without typically causing adverse effects to the plants, for a substantial part of their life cycle, and are primarily known for their beneficial role to their host plant [...

Synthetic plant microbiota challenges in nonmodel species

Plant-associated microbiota are becoming central in the development of ways to improve plant productivity and health. However, most research has focussed mainly on a few model plant species. It is essential to translate discoveries to the many nonmodel crops, allowing the design and application of effective synthetic microbiota

Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium—Plant Interaction

Many molecular signals are exchanged between rhizobia and host legume plants, some of which are crucial for symbiosis to take place, while others are modifiers of the interaction, which have great importance in the competition with the soil microbiota and in the genotype-specific perception of host plants. Here, we review recent findings on strain-specific and host genotype-specific interactions between rhizobia and legumes, discussing the molecular actors (genes, gene products and metabolites) which play a role in the establishment of symbiosis, and highlighting the need for research including the other components of the soil (micro)biota, which could be crucial in developing rational-based strategies for bioinoculants and synthetic communities’ assemblage