Learning on how to live in two contrasting worlds: The case of plant-associated soil bacteria

LAGARES A.

Oeiras, Portugal

Congreso; Congreso binacional BeMiPlant - 2022 (Beneficial Plant-Microbe Interactions - 2022), I Spanish-Portuguese Congress on Beneficial Plant-Microbe Interactions.; 2022

Congreso binacional, organizaron SEFIN (España) - INIAV (Portugal)

Prokaryotes constitute the oldest life forms on earth and represent true living fossils who help the reconstruction of the most ancestral processes of the biologic evolution. Prokaryotes are found as planktonic bacteria as well as cells intimately associated with other life forms—including plants—where the two constitute a holobiont. Both the numerosness of prokaryotes and their ability to horizontally exchange genes (i. e., the capability of sharing previous experiences) has proven to be an efficient strategy for loading the bacterial pangenomes with redundancy, thus minimizing the loss of information and maximizing cell diversity and survival. By using such communal architecture, prokaryotes support an extraordinary collection of adaptive responses, consistent with the remarkably high ratio of their environment-exposed surface to their cellular volume. In such a general evolutionary context, plant-associated soil bacteria have accommodated—and in some instances expanded—their genomes in order to live under such contrasting and challenging circumstances as those represented by the oligotrophic soil and the particularly carbon-rich plant niche.In this presentation I will focus on a few selected topics pointing to the way we have studied adaptive responses in soil bacteria covering specific instances of both their “free” and their associative life-styles. I will also discuss more general and basic forms of adaptation such as those involving the improvement of the genetic language.In order to investigate adaptive processes in a reference soil alpha-proteobacterium we studied: (a) how cells responded to a model abiotic stress (acidity) and to the associated changes, and (b) how bacteria faced the challenge represented by the presence of rhizospheres, an ecologic paradigm of nutrient abundance for which bacteria from the bulk soil compete with each other. Our multiomic and functional studies revealed the central pathways that were necessary for improving bacterial fitness under low pH (Draghi et al., 2016), suggesting also the existence of a possible associative learning connecting the low pH signal in batch cultures to the expression of a more proficient plant invasion (Draghi et al., 2010). Bacteria thus appeared to be prepared not only to face the low pH per se but also to anticipate a response to circumstances that were likely to occur, such as a decrease in the number of roots and their responses to bacteria at low pH—indeed, anticipation is the minimal concept of learning. We do not yet know whether changes in the increased ability of acid-adapted bacteria to infect plants are derived from an improved capability of colonizing the rhizosphere, of penetrating root tissues more efficiently, or both. Independent experiments involving a phenomic approach demonstrated that the colonization of plant roots in our model alpha-proteobacterium was influenced by ca. 2% of the genome (more than 140 genes), thus pointing to the relevance of the bacterial interaction with plants (Salas et al., 2017). The chromosomal location of most of these genes highlighted the ancestral character of the bacterial approach to roots, with some novel traits expressing preferential colonization of specific rhizospheres having emerged more recently, that time being likely ca. 30 million years ago in the linage that we studied (fewer than 10% of the genes that we found affected specifically the colonization of particular plant rhizospheres as opposed to others).Besides all these specific responses to environmental signals, we studied other more general adaptive strategy related to the way the language of the genetic code is used in bacteria. Languages are communication systems—either natural or formally created—that aim at the transmission of information between two physical and/or biologic entities: i. e., languages are systems for the transfer of meaningful data. While spoken communication among humans has been the most thoroughly studied natural language, the genetic-code–based transmission of information constitutes, by far, the most ancient and ubiquitous natural language, and one that is also common (almost universal) and essential to all life forms as well as to viruses. This circumstance, and the early observation that cells do not make random use of codons with isoacceptor tRNAs, stimulated numerous investigations to understand the mutational and selective phenomena associated with the differential codon (“word”) choices in organisms with remarkable differences in their global genomic compositions (GC contents spanning from less than 20% to ca. 80%).In order to investigate the trends and principles underlying specific codon preferences in the prokaryotic tree of life, we performed a comprehensive analysis of 29 different families within the domains Bacteria and Archaea and found 4 distinct behavioral groups (López et al., 2020). The analysis of core-gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly expressed genes exhibited the most optimized codon usage, the singletons always contained the less selectively favored codons. In agreement with previous reports, a C bias in 2- to 3-fold pyrimidine-ending codons, and a U bias in 4-fold codons occurred in all families, irrespective of the global genomic GC content. The U biases suggested that U3-mRNA–U-tRNA interactions were responsible for a prominent codon optimization in both the most ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved or variable translated products—with each one being under high and low expression levels—demonstrated that efficiency was more relevant (by a factor of 2) than was accuracy in the modelling of codon usage. Finally, after studying a model multipartite prokaryote genome, we performed a comprehensive analysis describing the inter- and intrareplicon heterogeneity of codon usages (López et al., 2019). Under the current view of the way cells make use of the 64 elements of their genetic code, novel parallels have to be elaborated to translate and contrast the classical definitions from cognitive language—like redundancy, synonymy (do fully synonymous codons exist?), ambiguity/polysemy (such as that associated with UGA codons) and contextual effects—all referring to different instances of plurality. That exercise will assist in understanding the minimal biologic needs and requirements that arose throughout evolution for the progressive emergence of specific semantic effects.ReferencesDraghi, W.O., Del Papa, M.F., Pistorio, M., Lozano, Giusti, M.A., Torres Tejerizo, G.A., Jofré, E., Boiardi, J.L., Lagares, A. (2010). Cultural conditions required for the induction of an adaptive acid-tolerance response (ATR) in Sinorhizobium meliloti and the question as to whether or not the ATR helps rhizobia improve their symbiosis with alfalfa at low pH. FEMS Microbiol Lett 302, 123-30, doi: 10.1111/j.1574-6968.2009.01846.xDraghi, W.O., Del Papa, M.F., Hellweg ,C., Watt, S.A., Watt, T.F., Barsch, A., Lozano, M.J., Lagares, A. Jr, Salas, M.E., López, J.L., Albicoro, F.J., Nilsson, J.F., Torres Tejerizo, G.A., Luna, M.F., Pistorio, M., Boiardi, J.L., Pühler, A., Weidner, S., Niehaus, K., Lagares, A. (2016). A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti. Sci Rep. 6, 29278, doi: 10.1038/srep29278López, J.L., Lozano, M.J., Fabre, M.L., Lagares, A. (2020). Codon usage optimization in the prokaryotic tree of life: How synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation. mBio 11, e00766-20, doi: 10.1128/mBio.00766-20López, J.L., Lozano, M.J., Lagares, A. Jr, Fabre, M.L., Draghi, W.O., Del Papa, M.F., Pistorio, M., Becker, A., Wibberg, D., Schlüter, A., Pühler, A., Blom, J., Goesmann, A., Lagares, A. (2019). Codon usage heterogeneity in the multipartite prokaryote genome: Selection-based coding bias associated with gene location, expression level, and ancestry. mBio 10, e00505-19, doi: 10.1128/mBio.00505-19.Salas, M.E., Lozano, M.J., López, J.L., Draghi, W.O., Serrania, J., Torres Tejerizo, G.A., Albicoro, F.J., Nilsson, J.F., Pistorio, M., Del Papa M.F., Parisi, G., Becker, A., Lagares, A. (2017). Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization. Environ Microbiol 19, :3423-3438, doi: 10.1111/1462-2920.13820AcknowledgementsResults included in this summary are part of the work performed by fellows and researches at the Laboratory of Genomics and Molecular Ecology of Plant-Associated Soil Microorganisms, IBBM. The work was supported by grants from CONICET, UNLP, MinCyT (all from Argentina), DAAD, Alexander von Humboldt Foundation (both from Germany), and the EC.