Studies on bacterial plant diseases have thus far been focused on the single bacterial species causing the disease, with very little attention given to the many other microorganisms present in the microbiome. This study intends to use pathobiome analysis of the rice foot rot disease, caused by Dickeya zeae, as a case study to investigate the effects of this bacterial pathogen to the total resident microbiome and to highlight possible interactions between the pathogen and the members of the community involved in the disease process. The microbiome of asymptomatic and the pathobiome of foot-rot symptomatic field-grown rice plants over two growing periods and belonging to two rice cultivars were determined via 16S rRNA gene amplicon sequencing. Results showed that the presence of D. zeae is associated with an alteration of the resident bacterial community in terms of species composition, abundance and richness, leading to the formation of microbial consortia linked to the disease state. Several bacterial species were significantly co-presented with the pathogen in the two growing periods suggesting that they could be involved in the disease process. Besides, culture-dependent isolation and in planta inoculation studies of a bacterial member of the pathobiome, identified as positive correlated with the pathogen in our in silico analysis, indicated that it benefits from the presence of D. zeae. A similar microbiome/pathobiome experiment was also performed in a symptomatically different rice disease evidencing that not all plant diseases have the same consequence/relationship with the plant microbiome. This study moves away from a pathogen-focused stance and goes towards a more ecological perception considering the effect of the entire microbial community which could be involved in the pathogenesis, persistence, transmission and evolution of plant pathogens.

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Pesticide residues in the soil are a huge threat to agriculture. ɤ- hexachlorocyclohexan (Lindane or isomer ɤ -HCH) is one of the pesticides widely used in agriculture after 1945. Due to the harmful effects on health of Lindane, UNEP (United Nations Environment) Program - United Nations Environment Program) decided to stop the pollution of Lindane worldwide in 2005. However, with a long half-life, it is very difficult to control residual Lindane in soils. The purpose of this study is to isolate and select actinomycete strains capable of degrading Lindane in order to develop a biological product that can remove residual Lindane in agricultural soil in a safe and environmental-friendly manner. Basic actinomycete isolation methods have been applied in combination with a number of oriented isolation methods to evaluate the growth ability of actinomycetes on media with and without Lindane. The ability to degrade Lindane of actinomycetes was also evaluated based on the rate of chloride ion removal in the substrate. The remarkable actinomycetes were then studied for biological characteristics such as morphology, biochemical and physiological properties, and some metabolic activities related to the degradation of Lindane. We obtained 9 actinomycetes capable of decomposing Lindane isolated from soil samples in farms in Nghe An. Among them, the two strains A119 and LD02 belonging to the genus Streptomyces displayed the best Lindane degradation performance based on their chloride ion removals. They were further studied for their biological characteristics and eventually identified.  

Kombucha beverage is a traditional and popular natural fermented beverage consumed across the globe. Kombucha beverage is produced by fermenting sweetened black tea, sucrose with consortium of acetic acid bacteria and yeasts. It is important to understand the microbial composition in Kombucha to facilitate better control of the fermentation process. Therefore, this study characterized the dominant acetic acid bacteria in Kombucha sample. Acetic acid bacteria isolated from the Kombucha using glucose-ethanol medium. Based on morphological, biochemical characterization, and 16S rRNA gene, 14 isolated strains belong to 2 species and were identified as Komagataeibacter saccharivorans and Komagataeibacter rhaeticus. These strains showed good biofilm forming abilities. Furthermore, the antimicrobial activity against five pathogenic bacteria including Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, Samonella enterica ATCC 13076, Pseudomonas aeruginosa ATCC 27853, Bacillus cereus ATCC 14579 of isolated acetic acid bacteria strains was also determined.  

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