Recent molecular studies on endophytic bacterial diversity have revealed a large richness of species. Endophytes promote plant growth and yield, suppress pathogens, may help to remove contaminants, solubilize phosphate, or contribute assimilable nitrogen to plants. Some endophytes are seedborne, but others have mechanisms to colonize the plants that are being studied. Bacterial mutants unable to produce secreted proteins are impaired in the colonization process. Plant genes expressed in the presence of endophytes provide clues as to the effects of endophytes in plants. Molecular analysis showed that plant defense responses limit bacterial populations inside plants. Some human pathogens, such as Salmonella spp., have been found as endophytes, and these bacteria are not removed by disinfection procedures that eliminate superficially occurring bacteria. Delivery of endophytes to the environment or agricultural fields should be carefully evaluated to avoid introducing pathogens.

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Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.

Animal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.

Flavobacteria and Enterobacteriaceae have been previously reported as scale insect endosymbionts. The purpose of this work was twofold: first, to screen different scale insect families for the presence of these endosymbionts by PCR analyses and second, to elucidate the history of cophylogeny between these bacteria and the insects by analysing a portion of 16S rRNA and 18S rRNA gene sequences by two reconciliation tools, CoRe-PA and Jane. From a survey of 27 scale insects within seven families, we identified Flavobacteria and Enterobacteriaceae as coexisting in ten species that belong to the Ortheziidae, Monophlebidae, Diaspididae and Coccidae families, and we frequently found two closely related enterobacteria harboured in the same individual. Analyses performed with CoRe-PA and Jane suggest that Flavobacteria from the scale insects analysed have a unique origin, except for Candidatus Brownia rhizoecola (Flavobacteria of Pseudococcidae, Phenacoccinae), which seems to come from a nonscale insect. Nevertheless, cospeciation between Flavobacteria and scale insects is suggested only within the families Monophlebidae, Ortheziidae and Diaspididae, and host switches seem to have occurred from the ancestors of Monophlebidae and Ortheziidae to insects from families Coccidae, Lecanodiaspididae, Eriococcidae and Pseudococcidae. Our analyses suggest that Enterobacteriaceae underwent more evolutionary events (losses, duplications and host switches), and their phylogenies showed a lower proportion of congruent nodes between host and bacteria, indicating a more relaxed relationship with scale insects compared with Flavobacteria.

Rhizobium etli, which normally forms nitrogen-fixing nodules on Phaseolus vulgaris (common bean), is a natural maize endophyte. The genetic diversity of R. etli strains from bulk soil, bean nodules, the maize rhizosphere, the maize root, and inside stem tissue in traditional fields where maize is intercropped with P. vulgaris-beans was analyzed. Based on plasmid profiles and alloenzymes, it was determined that several R. etli types were preferentially encountered as putative maize endophytes. Some of these strains from maize were more competitive maize-root colonizers than other R. etli strains from the rhizosphere or from bean nodules. The dominant and highly competitive strain Ch24-10 was the most tolerant to 6-methoxy-2-benzoxazolinone (MBOA), a maize antimicrobial compound that is inhibitory to some bacteria and fungi. The R. tropici strain CIAT899, successfully used as inoculant of P. vulgaris, was also found to be a competitive maize endophyte in inoculation experiments.

The present study investigated bacterial diversity associated with the roots of maize through the use of culture-dependent and culture-independent methods. Bacterial 16S-23S rDNA internal transcribed spacer sequences (ITS) primers were used to amplify sequences obtained directly from the root matrix by Percoll gradient separation. This assay showed that γ-Proteobacteria within Enterobacter, Erwinia, Klebsiella, Pseudomonas, and Stenotrophomonas genera were predominant groups. The culturable component of the bacterial community was also assessed, revealing that the predominant group was Firmicutes, mainly of Bacillus genus, while Achromobacter, Lysinibacillus, and Paenibacillus genera were rarely found in association with the roots. Only two genera within γ-Proteobacteria, Enterobacter and Pseudomonas, were found in the culture collection. Differences in richness and diversity between the rhizospheric and endophytic bacterial communities were also evidenced. The spectrum of bacteria naturally associated with maize roots is wide and the magnitude of such diversity will depend on the methods chosen for analysis. The knowledge of this spectrum will facilitate the search of microorganisms capable of exerting antagonism to diverse pathogens or detecting plant growth enhancers.

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