![]() ![]() Finally, a noteworthy endophytic example within Alphaproteobacteria, is the nitrogen-fixing symbiosis established with leguminous plants by rhizobia, which is coupled with the development of a new plant structure, the nodule, in the root or in the stem of the plant. Obligate endophytes are strictly dependent on the host plant for their growth and survival and transmission to other plants could occur only by seeds or via vectors, while facultative endophytes could grow outside host plants. Endophytic bacteria can be defined as those bacteria that colonize the internal tissue of the plants (endosphere) with no external sign of infection or negative effect on their host they can be classified as ‘obligate’ or ‘facultative’ endophytes in accordance with their life strategies. The rhizosphere is the part of soil around plant roots populated by microbes (bacteria and fungi) microorganisms from the rhizosphere interact with roots in several process such as the decomposition of organic matter, the maintenance of soil structure and water relationships, as a consequence rhizosphere is a fundamental niche of the soil ecosystem. ![]() Phyllospheric bacteria inhabits the aerial parts of the plant (leaves, stems, buds, flowers and fruits), possibly affecting plant fitness and productivity of agricultural crops. Plant-associated bacteria sensu lato can be found in, and around roots, in the vasculature, and on aerial tissues or in specifically developed organs (e.g., root nodules), allowing to categorize strains as phyllospheric, rhizospheric and endophytic. Particularly intriguing is the alphaproteobacterial ability to interact with plants, as pathogens and as nonpathogenic mutualist/commensals (symbionts/nonsymbionts) (e.g., Rhizobium, Azospirillum). ![]() Because of these genomic traits, and also thanks to their versatility in adapting to different habitats, Alphaproteobacteria constitute an excellent model system to study how bacterial genomes evolve and how genomic features are related to environmental adaptation. Īlphaproteobacteria, with nearly 600 completely sequenced genomes, is one of the most studied bacterial classes, showing a large heterogeneity in genome size, from 1.1 to 9.2 Mbp and genome architecture, with the presence of additional replicons, such as chromids, and plasmids. Habitats that are colonized by Alphaproteobacteria, range from the ocean floor volcanic environments, to soil, in which they may interact with plant roots, to surface waters of oceans. In addition, mitochondria have a common origin with SAR11 clade, as a sister group of the order Rickettsiales. Within this group, the class of Alphaproteobacteria harbors a miscellaneous set of metabolisms, cellular phenotypes and a wide range of habitats, including phototrophic genera ( Rhodobacter), symbionts of plants ( Rhizobium, Sinorhizobium, Mesorhizobium and Azorhizobium ), animal and plant pathogens ( Rickettsia, Brucella, Agrobacterium) and also genera able to metabolize C1 compounds ( Methylobacterium). The phylum Proteobacteria is the most numerous group currently recognized in the domain Bacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. ![]()
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