Functional genomics analysis of a phyllospheric Pseudomonas spp with potential for biological control against coffee rust.

BACKGROUND: Pseudomonas spp. promotes plant growth and colonizes a wide range of environments. During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. In parallel, several experiments were performed to confirm certain physiological characteristics that could be associated with phyllospheric behavior. Finally, in vivo and in vitro experiments were carried out to verify whether this isolate could serve as a biocontrol agent against coffee rust and how the isolate could act against the infection.  RESULTS: The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. There was an increase of exopolysaccharides synthesis in response to osmotic stress, which may protect cells from dessication on phyllosphere. Metabolic pathways for degradation and incorporation into citrate cycle of phenolic compounds present in coffee were found, and experimentally confirmed. In addition, MN1F was found to be highly tolerant to caffeine. The experiments of biocontrol against coffee leaf rust showed that the isolate can control the progress of the disease, most likely through competition for resources. CONCLUSION: Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent.

Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean.

Angular leaf spot (ALS) is a disease that causes major yield losses in the common bean crop. Studies based on different isolates and populations have already been carried out to elucidate the genetic mechanisms of resistance to ALS. However, understanding of the interaction of this resistance with the reproductive stages of common bean is lacking. The aim of the present study was to identify ALS resistance loci at different plant growth stages (PGS) by association and linkage mapping approaches. An BC2F3 inter-gene pool cross population (AND 277 × IAC-Milênio - AM population) profiled with 1,091 SNPs from genotyping by sequencing (GBS) was used for linkage mapping, and a carioca diversity panel (CDP) genotyped by 5,398 SNPs from BeadChip assay technology was used for association mapping. Both populations were evaluated for ALS resistance at the V2 and V3 PGSs (controlled conditions) and R8 PGS (field conditions). Different QTL (quantitative trait loci) were detected for the three PGSs and both populations, showing a different quantitative profile of the disease at different plant growth stages. For the three PGS, multiple interval mapping (MIM) identified seven significant QTL, and the Genome-wide association study (GWAS) identified fourteen associate SNPs. Several loci validated regions of previous studies, and Phg-1, Phg-2, Phg-4, and Phg-5, among the 5 loci of greatest effects reported in the literature, were detected in the CDP. The AND 277 cultivar contained both the Phg-1 and the Phg-5 QTL, which is reported for the first time in the descendant cultivar CAL143 as ALS10.1UC. The novel QTL named ALS11.1AM was located at the beginning of chromosome Pv11. Gene annotation revealed several putative resistance genes involved in the ALS response at the three PGSs, and with the markers and loci identified, new specific molecular markers can be developed, representing a powerful tool for common bean crop improvement and for gain in ALS resistance.

Diferenciação de bactérias do gênero Pseudomonas patogênicas ao cafeeiro por técnicas serológicas / Differentiation of bacteria of the genus Pseudomonas pathogenic to coffee by serological techniques

Há várias bactérias que causam problemas para o cafeeiro, incluindo Pseudomonas cichorii, P. syringae pv. garcae, P. syringae pv. tabaci, Burkholderia andropogonis e Xylella fastidiosa, todas elas já descritas no Brasil. Tentativas de diferenciar essas bactérias por testes serológicos de dupla difusão em ágar (dda), com antissoros produzidos contra células íntegras de P. s. pv. garcae, mostraram reações cruzadas, principalmente entre P. s. pv. garcae e P. s. pv. tabaci. Dessa forma, foram produzidos antissoros contra P. s. pv. garcae (linhagem patotipo IBSBF-248 - Coleção de Culturas de Fitobactérias do Instituto Biológico - IBSBF), obtidos por meio de imunizações de coelhos com antígenos de proteínas do complexo proteico da membrana (CPM). Esses antissoros foram testados por dupla difusão em agarose (dda) contra diversas formas de antígenos extraídos de P. cichorii, P. s. pv. garcae e P. s. pv. tabaci [células autoclavadas, células tratadas com formol, exopolissacarídeos (EPS), glicoproteínas (GP) da cápsula bacteriana, proteínas de membrana e suspensão bacteriana (SB) em NaCl 0,85%]. Os resultados mostraram que, dependendo do antígeno e do meio suporte da dupla difusão (com ou sem MgCl2 e/ou azul de tripano), os antissoros reagem somente com P. s. pv. garcae. Desse modo, esses antígenos podem ser usados para a rápida diagnose da mancha aureolada do cafeeiro nos testes de dda.(AU)

Some bacterial diseases have been described causing problems in coffee, whose causal agents are Pseudomonas cichorii, P. syringae pv. garcae, P. s. pv. tabaci and Burkholderia andropogonis, all of them also occurring in Brazil. Attempts to differentiate these bacteria by double diffusion agar (dda) technique with antisera produced against whole cells of P. s. pv. garcae showed cross-reactions, especially among P. s. pv. garcae and P. s. pv. tabaci. Thus, antisera were produced against P. s. pv. garcae (pathotype strain IBSBF-248 - Phytobacteria Culture Collection of Instituto Biológico - IBSBF), using rabbit immunizations with antigens of the protein complex of membranes. These antisera were tested against different kind of antigens (autoclaved cells, cells treated with formaldehyde, capsule polysaccharides, glycoproteins, bacterial membrane proteins and bacterial suspension in 0.85% NaCl) extracted from P. cichorii, P. s. pv. garcae and P. s. pv. tabaci. The results showed that depending on the kind of antigen and the medium used in the double diffusion test (with or without MgCl2 and/or trypan blue), the antiserum reacted only with P. s. pv. garcae. Thus, these antigens may be used as an auxiliary tool in the rapid diagnosis of bacterial halo blight of coffee in the double diffusion test.(AU)