Bacterial organisms continuously maintain homeostasis even in changing environments. This ability to maintain homeostasis is especially critical for pathogenic and opportunistic bacteria, which must adapt to both abiotic and biotic host environments. Both types of environments present unique limitations and conditions. Transition metal homeostasis under these varying conditions is important for bacterial survival. Transition metals such as zinc, cobalt, iron and copper are essential for cell survival, but become toxic if in excess. The host organism often takes advantage of this requirement by greatly limiting access to transition metals to limit infections, but in other environments, toxic levels of metal may be present. Bacterial organisms have developed many mechanisms to maintain transition metal homeostasis. This study focuses on two bacterial systems that are utilized to maintain metal balance; the heme-acquiring iron surface determinant (Isd) system of Bacillus anthracis and the copper and silver export Cus system of Escherichia coli. Host organisms use many proteins and systems to limit iron access from pathogenic bacteria, known as nutrient immunity. B. anthracis must acquire iron from the host organism upon infection and so has evolved multiple iron acquisition systems. The Isd system employs two extracellular proteins, IsdX1 and IsdX2, to remove heme from hemoglobin to use as an iron source. Once bound to heme, these hemophores transfer heme to a cell surface attached protein, IsdC, which further relays the molecule to be transferred into the cell for iron use. This study focused on the kinetics of heme transfer to better understand how acquisition occurs. This study determined that the oxidation state of the iron-heme molecule plays a significant role in the kinetics of heme acquisition by IsdX1 and subsequent transfer to IsdC. This work clarifies and further establishes the mechanism of iron acquisition by B. anthracis during infection. Copper and silver are used in many settings as antimicrobial agents, including as an alternative to antibiotic drugs. Pathogenic and opportunistic bacteria, such as E. coli, experience stress upon contact with copper and silver surfaces and materials. Copper is an essential transition metal, while silver is not biologically used, but both become toxic when in excess due to redox properties and disruption of biological molecules. E. coli utilizes several systems to remove excess copper and silver to resist toxicity. The Cus system, consisting of the soluble CusF and tripartite pump CusCBA, specifically exports copper and silver from the periplasm. Several roles of CusF have been suggested from in vitro data. The components CusAB were hypothesized to be the essential proteins of the CusCBA pump, while the outer membrane unit may not contribute specificity or be necessary for export. This study focused on the role and importance of CusF and outer membrane channel CusC during copper stress in vivo. An in vivo interaction between CusF and CusB was identified during copper stress. The data from this work indicate that cusF and cusC directly affect intracellular copper accumulation. Furthermore, this study revealed that SdsP may play in a secondary role to CusC to complement CusC to maintain copper resistance. This works establishes the importance of CusC as the main outer membrane component during copper export in E. coli.

Made available in DSpace on 2014-06-11T19:23:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-11-16Bitstream added on 2014-06-13T19:28:59Z : No. of bitstreams: 1 ucci_ap_me_araiq.pdf: 1107212 bytes, checksum: d5908c197d6d3cb915d0549cd1755e02 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Xanthomonas citri subsp. citri (Xcc) é uma bactéria Gram-negativa responsável pelo o cancro cítrico. A doença causada por este fitopatógeno constitui numa das mais graves doenças da citricultura brasileira, cujas medidas de controle capazes de eliminar completamente a doença são ineficientes até o momento. O sequenciamento e anotação do genoma de Xcc juntamente com estudos relacionados à genômica funcional nesta bactéria realizados em nosso laboratório mostraram a existência, na bactéria, de alguns genes (copA e copB) que codificam proteínas envolvidas com o mecanismo de resistência a cobre (CopA e CopB). Os genes que codificam ambas proteínas estão organizados em um operon, cuja transcrição é induzida por cobre e é específica ao metal. Componentes a base de cobre são comumente usados na agricultura como agentes microbicidas a fim de reduzir a severidade desta e também de outras doenças nas plantas. Contudo, a eficácia do cobre está sendo reduzida pelo aparecimento de linhagens de bactérias resistentes a este metal, portanto, estudos visando a compreensão dos mecanismos moleculares envolvidos na resistência a cobre em Xcc são de grande importância. Uma pequena ORF (XAC3629) que codifica uma proteína hipotética de 152 aminoácidos e que se localiza upstream aos genes copAB foi identificada. Neste trabalho foi estudado o papel da ORF na regulação do operon copAB. Linhagens mutantes contendo a ORF XAC3629 interrompida por um transposon (XAC3629 / Xanthomonas citri subsp. citri (Xcc) is a Gram-negative bacterium that causes citrus canker, one of the most serious diseases in Brazilian crops, and the ways to eliminate it are not efficient. After sequencing and annotation of the Xcc genome our laboratory started to perform functional genomic studies in Xcc. Previous studies identified two genes (copA and copB) that encode proteins involved in the copper resistance mechanism (CopA and CopB). The genes are organized in an operon whose transcription is induced and specific to copper. Copper compounds are commonly used in agriculture in order to control plant diseases, however the copper effectiveness is being reduced due to the emergence of copper resistant bacteria strains. Therefore, studies related to copper resistance mechanism in Xcc are very relevant. A short ORF (XAC3629) which encodes an 152 amino acids hypothetical protein was identified upstream the operon copAB. In this work the role of the ORF in the operon regulation was studied. Mutant strains containing the ORF XAC3629 interrupetd by a transposon (XAC3629

Orientador: Maria Célia Bertolini / Banca: Jesus Aparecido Ferro / Banca: Julio Cezar Franco de Oliveira / Resumo: Xanthomonas citri subsp. citri (Xcc) é uma bactéria Gram-negativa responsável pelo o cancro cítrico. A doença causada por este fitopatógeno constitui numa das mais graves doenças da citricultura brasileira, cujas medidas de controle capazes de eliminar completamente a doença são ineficientes até o momento. O sequenciamento e anotação do genoma de Xcc juntamente com estudos relacionados à genômica funcional nesta bactéria realizados em nosso laboratório mostraram a existência, na bactéria, de alguns genes (copA e copB) que codificam proteínas envolvidas com o mecanismo de resistência a cobre (CopA e CopB). Os genes que codificam ambas proteínas estão organizados em um operon, cuja transcrição é induzida por cobre e é específica ao metal. Componentes a base de cobre são comumente usados na agricultura como agentes microbicidas a fim de reduzir a severidade desta e também de outras doenças nas plantas. Contudo, a eficácia do cobre está sendo reduzida pelo aparecimento de linhagens de bactérias resistentes a este metal, portanto, estudos visando a compreensão dos mecanismos moleculares envolvidos na resistência a cobre em Xcc são de grande importância. Uma pequena ORF (XAC3629) que codifica uma proteína hipotética de 152 aminoácidos e que se localiza upstream aos genes copAB foi identificada. Neste trabalho foi estudado o papel da ORF na regulação do operon copAB. Linhagens mutantes contendo a ORF XAC3629 interrompida por um transposon (XAC3629::Tn), previamente construídas no laboratório, foram avaliadas em relação ao crescimento em meio contendo diferentes concentrações de cobre. Estas linhagens mostraram perda da resistência quando o metal foi adicionado ao meio, mesmo em baixas concentrações (0,25 mM), sugerindo seu envolvimento na regulação do operon de resistência a cobre copAB. Células da linhagem selvagem ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Xanthomonas citri subsp. citri (Xcc) is a Gram-negative bacterium that causes citrus canker, one of the most serious diseases in Brazilian crops, and the ways to eliminate it are not efficient. After sequencing and annotation of the Xcc genome our laboratory started to perform functional genomic studies in Xcc. Previous studies identified two genes (copA and copB) that encode proteins involved in the copper resistance mechanism (CopA and CopB). The genes are organized in an operon whose transcription is induced and specific to copper. Copper compounds are commonly used in agriculture in order to control plant diseases, however the copper effectiveness is being reduced due to the emergence of copper resistant bacteria strains. Therefore, studies related to copper resistance mechanism in Xcc are very relevant. A short ORF (XAC3629) which encodes an 152 amino acids hypothetical protein was identified upstream the operon copAB. In this work the role of the ORF in the operon regulation was studied. Mutant strains containing the ORF XAC3629 interrupetd by a transposon (XAC3629::Tn) were previously constructed in our laboratory and in this work their growth were evaluated in a medium containing different copper concentration. The mutant strains were unable to grow when the metal was added to the medium, even at low concentration (0.25 mM) suggesting that the ORF XAC3629 may have a role in regulating the operon copAB. Wild type Xcc cells are able to grow up to 1 mM copper concentration. Attempts to construct an ORF XAC3629 knocked out strain were performed but this mutant strain was not obtained. Two XAC3629::Tn mutants strains were transformed with a plasmid construction containing the ORF XAC3629 entire sequence plus its flanking regions. The results did not show functional complementation (recovery of the copper resistance when cells were grown in medium containing ... (Complete abstract click electronic access below) / Mestre

Copper cast alloys de-activate antibiotic-resistant bacteria on contact and could be very effective in decreasing potentially harmful microorganisms in the environment. In this study copper alloys with varying copper contents were utilized to evaluate their antimicrobial effects on Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecium in changing environmental conditions. The survival rates of P. aeruginosa wild type and its derivative transposon mutants of the cin operon on copper cast alloys were investigated in order to demonstrate the influence of genes involved in copper resistance. The gene disruption of the response regulator of the cin operon resulted in shorter survival rates on copper alloys, which was also influenced by temperature and method of exposure. Bacteria often have acquired copper resistance mechanisms in order to withstand higher copper concentrations in their surroundings, which may be a factor in their survival rates on copper surfaces. Copper- and antibiotic-resistant E. coli and E. faecium strains were obtained from pigs raised on feeds containing copper sulfate and antibiotics. Survival rates of these bacteria were influenced by the percentage of copper in the alloys, varying moisture conditions on copper surfaces, suspension media used, and differences between strains. Survival was also dependent on copper corrosion rates since corrosion inhibition with benzotriazole or a thick surface layer of thermal oxide resulted in prolonged survival on copper surfaces. Corrosion of copper surfaces releases copper ions which directly affect bacterial survival on copper alloys. The results obtained in this study emphasize that copper alloys are effective as antimicrobial materials but changing environmental conditions can significantly influence bacterial survival on copper surfaces. These findings can be applied to a better utilization of copper alloys in water, food, and healthcare environments. Antibiotic- and copper ion-resistant bacteria can be killed on contact with copper alloys which makes the proliferation of these microorganisms less likely and reduces the risk to human health. However, in a very different environment copper ion-resistant microbes can be useful for plant-microbe associations in bioremediation of copper mining wastelands.

Este trabalho teve como objetivo caracterizar a diversidade bacteriana presente em uma área de mineração. Os resultados mostraram que o filo mais abundante das bactérias classificadas foi o proteobacteria e 66% deste filo pertencem a classe betaproteobacteria. A diversidade de bactérias encontradas no solo de fora da mina mostrou-se diferente daquele encontrado dentro da mina, mostrando que a ação da mineração poderia ter modificado a comunidade microbiana nativa do local. Na tentativa de elucidar o mecanismo de resistência ao cobre presente nos isolados, foram escolhidas 2 cepas resistentes a altas concentrações de cobre: Acinetobacter sp. e Enterobacter sp. Os resultados de proteômica mostraram que as duas cepas possuem mecanismos diferentes de resistência. Acinetobacter teve a expressão de duas proteínas CopA e CopB em diferentes condições de cultivos (200 ppm de cobre 6h de cultivo; 24h e 72h de cultivo em 450 ppm de cobre). Com esses resultados foi possível elucidar que esta cepa tem o mesmo mecanismo de resistência encontrado em Enterococcus hirae, onde a proteína CopA tem como função o influxo de cobre e a proteína CopB o efluxo do excesso de cobre intracelular. Já a bactéria Enterobacter teve expressão apenas de proteínas de membranas e nenhuma proteína propriamente conhecida como de resistência à cobre. Este resultado foi corroborado por técnica de PCR, no qual não houve expressão para esse gene. Possivelmente as proteínas de membrana externa estão responsáveis pela homeostase do cobre realizada por esta cepa. / This work aimed to characterize the bacterial diversity present in a mining area. Results showed the most abundant phylum of the classified bacteria are proteobacteria and 66% of this phylum are class betaproteobacteria. The diversity of bacteria found in the soil outside the mine differed from those found within the mine, showing that the mining action may have modified the local microbial community. In an attempt to elucidate the mechanism of resistance to copper present in the isolates, two strains resistant to high concentrations of copper were chosen: Acinetobacter sp. and Enterobacter sp. Proteomics results showed these two strains have different mechanisms of resistance. Acinetobacter had the expression of two CopA and CopB proteins under different cultivation conditions (200 ppm of copper 6h of culture and 24h and also in 450 ppm of copper and 72h of culture). With these results it was possible to elucidate, this strain has the same mechanism of resistance found in Enterococcus hirae, which the CopA protein functions as the copper influx and the CopB protein the efflux of excess intracellular copper. On the other hand, Enterobacter bacterium had only membrane proteins, and no proteins known as copper resistance. This result was corroborated with PCR, where there was no expression for this gene. Possibly the outer membrane proteins are responsible for the copper homeostasis performed by this strain.

Este trabalho teve como objetivo caracterizar a diversidade bacteriana presente em uma área de mineração. Os resultados mostraram que o filo mais abundante das bactérias classificadas foi o proteobacteria e 66% deste filo pertencem a classe betaproteobacteria. A diversidade de bactérias encontradas no solo de fora da mina mostrou-se diferente daquele encontrado dentro da mina, mostrando que a ação da mineração poderia ter modificado a comunidade microbiana nativa do local. Na tentativa de elucidar o mecanismo de resistência ao cobre presente nos isolados, foram escolhidas 2 cepas resistentes a altas concentrações de cobre: Acinetobacter sp. e Enterobacter sp. Os resultados de proteômica mostraram que as duas cepas possuem mecanismos diferentes de resistência. Acinetobacter teve a expressão de duas proteínas CopA e CopB em diferentes condições de cultivos (200 ppm de cobre 6h de cultivo; 24h e 72h de cultivo em 450 ppm de cobre). Com esses resultados foi possível elucidar que esta cepa tem o mesmo mecanismo de resistência encontrado em Enterococcus hirae, onde a proteína CopA tem como função o influxo de cobre e a proteína CopB o efluxo do excesso de cobre intracelular. Já a bactéria Enterobacter teve expressão apenas de proteínas de membranas e nenhuma proteína propriamente conhecida como de resistência à cobre. Este resultado foi corroborado por técnica de PCR, no qual não houve expressão para esse gene. Possivelmente as proteínas de membrana externa estão responsáveis pela homeostase do cobre realizada por esta cepa. / This work aimed to characterize the bacterial diversity present in a mining area. Results showed the most abundant phylum of the classified bacteria are proteobacteria and 66% of this phylum are class betaproteobacteria. The diversity of bacteria found in the soil outside the mine differed from those found within the mine, showing that the mining action may have modified the local microbial community. In an attempt to elucidate the mechanism of resistance to copper present in the isolates, two strains resistant to high concentrations of copper were chosen: Acinetobacter sp. and Enterobacter sp. Proteomics results showed these two strains have different mechanisms of resistance. Acinetobacter had the expression of two CopA and CopB proteins under different cultivation conditions (200 ppm of copper 6h of culture and 24h and also in 450 ppm of copper and 72h of culture). With these results it was possible to elucidate, this strain has the same mechanism of resistance found in Enterococcus hirae, which the CopA protein functions as the copper influx and the CopB protein the efflux of excess intracellular copper. On the other hand, Enterobacter bacterium had only membrane proteins, and no proteins known as copper resistance. This result was corroborated with PCR, where there was no expression for this gene. Possibly the outer membrane proteins are responsible for the copper homeostasis performed by this strain.

Doctor of Philosophy / Department of Diagnostic Medicine and Pathobiology / Harvey Morgan Scott / The use of antibiotics in food animals is of major concern as a purported cause of antimicrobial resistance (AMR) in human pathogens; as a result, alternatives to in-feed antibiotics such as heavy metals have been proposed. The effect of copper and CTC supplementation in weaned pigs on AMR in the gut microbiota was evaluated. Four treatment groups: control, copper, chlortetracycline (CTC), and copper plus CTC were randomly allocated to 32 pens with five pigs per pen. Fecal samples (n = 576) were collected weekly from three pigs per pen over six weeks and two Escherichia coli isolates per sample were tested phenotypically for antimicrobial and copper susceptibilities and genotypically for the presence of tetracycline (tet), copper (pcoD) and ceftiofur bla[subscript]C[subscript]M[subscript]Y₋₂) resistance genes. CTC-supplementation significantly increased tetracycline resistance and susceptibility to copper when compared with the control group. Copper supplementation decreased resistance to most of the antibiotics, including cephalosporins, over all treatment periods. However, copper supplementation did not affect minimum inhibitory concentrations of copper or detection of pcoD. While tetA and bla[subscript]C[subscript]M[subscript]Y₋₂ genes were associated with a higher multi-drug resistance (MDR), tetB and pcoD were associated with lower MDR. Supplementations of CTC or copper alone were associated with increased tetB prevalence; however, their combination was paradoxically associated with reduced prevalence. These studies indicate that E. coli isolates from the weaned pigs studied exhibit high levels of antibiotic resistance with diverse multi-resistant phenotypic profiles. In a related study, total fecal community DNA (n = 569) was used to detect 14 tet genes and to quantify gene copies of tetA, tetB, pcoD and bla[subscript]C[subscript]M[subscript]Y₋₂. CTC and copper plus CTC supplementation increased both the prevalence and gene copies of tetA, while decreasing both the prevalence and gene copies of tetB, when compared with the control group. The diversity of tet genes were reduced over time in the gut bacterial community. The roles of copper supplementation in pig production and pco-mediated copper resistance in E. coli need to be further explored since a strong negative association of pcoD, with both tetA and bla[subscript]C[subscript]M[subscript]Y₋₂, suggests there exist opportunities to select for a more innocuous resistance profile.

La galle du collet, caractérisée par la formation d'une tumeur, représente la bactériose la plus répandue chez la vigne et entraine d'importantes pertes économiques à travers le monde. L'agent responsable de cette maladie est le plasmide Ti (pTi) qui confère à ces bactéries hôtes, telles que des Allorhizobium vitis, leur pouvoir pathogène. En plus du pTi, les A. vitis sont aussi les hôtes d'autres plasmides dont les fonctions et les modes de dissémination sont peu documentés. Afin d'étudier l'adaptation particulière des souches d'A. vitis à la vigne, nous nous sommes intéressés à la diversité de ces pathogènes ainsi qu'au rôle de ces plasmides et à la régulation de leur dissémination. Tout d'abord, nous avons analysé la diversité des isolats provenant de vignobles du Maroc atteints par la galle du collet. Nous avons pu mettre en évidence que l'ensemble des isolats pathogènes (e.g. porteur d'un pTi) forme 4 groupes génétiques se distinguant par le type d'opine produit. Nous nous sommes par la suite intéressés à la souche A. vitis S4 qui héberge 5 plasmides dont 3 possèdent un mécanisme de transfert pouvant être régulé par un système de communication bactérienne nommé quorum sensing (QS). Nous avons montré que le système QS du plasmide p130 (renommé pApi) contrôle non seulement le transfert conjugatif du pApi mais aussi d'autres fonctions plasmidiques non caractérisées. Ce système QS nécessite la synthèse d'une molécule signal de type N-acyl-homosérine lactone qui d'après nos travaux de caractérisation possède une structure atypique. De plus, des analyses génomiques couplées à des tests de résistance au cuivre nous ont permis d'identifier, sur le plasmide p79 d'A. vitis S4, un îlot de gènes potentiellement impliqués dans la résistance au cuivre de cette souche. Via des analyses de diversité ainsi que l'étude d'une souche modèle, nos travaux fournissent des connaissances sur l'adaptation d'Allorhizobium vitis à son unique plante hôte, la vigne / Crown gall disease, characterized by the formation of a tumor, represents the most widespread bacteriosis in the vineyard and causes significant economic losses throughout the world. The causing agent is the Ti plasmid (pTi) which confers pathogenicity to their bacterial hosts, such as Allorhizobium vitis. In addition to pTi, A. vitis harbours other plasmids whose functions and ways of dissemination are poorly documented. In order to study the peculiar adaptation of A. vitis strains to grapevine, we studied the diversity of these pathogens as well as the role of plasmids and the regulation of their dissemination.First, we analyzed the diversity of isolates from vineyards of Morocco affected by crown gall. We highlighted that all the pathogenic isolates (e.g. carrying a pTi) form 4 genetic groups that are distinguished by the type of opine produced and the ability to induce a hypersensitive response. We then focused on strain A. vitis S4, which contains 5 plasmids, including 3 possessing a transfer mechanism that can be regulated by a bacterial communication system called quorum sensing (QS). We demonstrated that the QS system of plasmid p130 (renamed pApi) controls not only the conjugative transfer of the pApi but also other uncharacterized plasmid-encoded functions. This QS system requires the synthesis of a N-acyl-homoserine lactone signal molecule with an atypical structure. In addition, genomic analyzes combined with copper resistance assays allowed us to identify, on plasmid p79 of A. vitis S4, a genomic island that is likely involved in copper resistance of this strain.Through analyzes of diversity and study of a model strain, our work provides insight into adaptation of Allorhizobium vitis to its unique host plant, grapevine

Le cuivre, souvent utilisé pour gérer les bactérioses en agriculture, est largement utilisé dans la lutte contre Xanthomonas citri pv. citri (Xcc), agent responsable du chancre asiatique des agrumes. La récente détection d’un phénotype résistant au cuivre (CuR) chez Xcc dans deux territoires ultramarins français a motivé une étude génomique qui a révélé, dans les génomes de souches CuR, la présence d’un plasmide conjugatif portant un transposon adaptatif de type Tn3. Sa conservation chez plusieurs espèces de Xanthomonas phytopathogènes suggère le rôle des transferts horizontaux (HGT) dans l’adaptation de Xcc. Nous avons donc analysé, dans l’océan Indien, les relations phylogénétiques de souches sensibles et CuR en prenant en compte à la fois les SNP et les variations de contenu en gènes. La datation de la phylogénie a permis de formuler des scenarii d’introduction de la bactérie dans la région. La phylogénie a montré une structure géographique forte à l’échelle de l’océan Indien, qui s’estompe à l’échelle de la Réunion et disparaît à l’échelle du verger. Au sein des vergers, l’admixture est un élément favorable aux HGT entre souches génétiquement différentes. Ils sont pourtant peu caractérisés chez les bactéries du genre Xanthomonas. Nous avons ainsi analysé la dispersion de l’ensemble des gènes plasmidiques connus de la famille des Xanthomonadaceae dans l’ensemble des génomes bactériens de NCBI, mettant en évidence à la fois la forte prévalence des gènes plasmidiques au sein des Xanthomonadaceae mais aussi la limite taxonomique forte à leur échange par conjugaison. L’importance du mosaïsme plasmidique, en partie lié aux éléments mobiles a aussi été illustrée. L’ensemble de nos résultats souligne l’importance des HGT dans l’évolution des bactéries du genre Xanthomonas, et la nécessité de caractériser finement le contenu et le fonctionnement du génome environnemental des Xanthomonadaceae pour appréhender au mieux l’adaptation de ces bactéries phytopathogènes. / Copper, frequently used in agriculture to control bacterial diseases, is commonly used against Xanthomonas citri pv. citri (Xcc), the bacterial agent of Asiatic citrus canker. The recent detection of a copper-resistant phenotype in two French overseas regions motivated a genomic study which revealed, in copper-resistant (CuR) strains, a conjugative plasmid encoding an adaptive transposon of the Tn3 family. Its conservation in several Xanthomonas species suggested the role of horizontal gene transfer (HGT) in Xcc adaptation. We therefore analyzed the evolutionary history of susceptible and CuR Xcc strains in the Indian Ocean using both SNP and gene content variations. The dating of the obtained phylogeny allowed us to hypothesize the history of Xcc introduction into the region. The phylogeny showed a strong geographic structure among islands of the Indian Ocean region, which faded at the Réunion scale and disappeared at the grove scale. Among the groves, admixture is a factor favoring HGT between genetically distinct strains. This form of evolution is however largely uncharacterized in the Xanthomonas genus. To fill this gap, we searched genetic homology between the whole known plasmid gene content of the Xanthomonadaceae family and the complete set of genomes hosted in NCBI databases. We highlighted both the ubiquity of plasmid genes in the Xanthomonadaceae family and the taxonomical barrier of their sharing by conjugation. The small fraction of genes that were exchanged through the complete sharing of plasmids also revealed the importance of plasmid mosaicism, partly due to mobile genetic elements. Taken together, our results highlight the importance of bacterial communities in the evolution of phytopathogenic bacteria of the Xanthomonas genus, and the need for a precise characterization of the content and the functioning of the Xanthomonadaceae environmental genome in order to fully apprehend the adaptation of these phytopathogenic bacteria.