Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri

Background: Gene expression analysis via microarray is widely used in phytobacteria to validate differential gene expression associated with virulence or to compare biological profiles of wild type and mutant strains. Here, we employed DNA microarrays to study the early stages of the infection process (24, 72 and 120 h post-inoculation) of Xanthomonas citri subsp. citri (Xac) infecting Citrus sinensis to interrogate the expression profiles of hypothetical genes. Results: Under infective conditions, 446 genes were up- and 306 downregulated. Outstanding among genes upregulated during infection were those involved in synthesizing the Type 3 Secretion System and effectors, xanthan gum and quorum-sensing induction, and flagellum synthesis and regulation. Additionally, 161 hypothetical genes were up- and 100 were downregulated, 49 of which are known to have a significant biological role. To understand hypothetical gene co-regulation or -expression, nine expression profiles including 158 genes were identified during the three infection phases. Of these, 47 hypothetical genes were identified as having expression profiles associated with at least one connected to a gene associated with adaptation and virulence. Conclusions: Expression patterns of six differentially expressed genes were validated by quantitative reverse transcription polymerase chain reaction, thus demonstrating the effectiveness of this tool in global gene expression analysis in Xac.

Predominance of syntrophic bacteria, Methanosaeta and Methanoculleus in a two-stage up-flow anaerobic sludge blanket reactor treating coffee processing wastewater at high organic loading rate.

The effect of the organic loading rate (OLR) on the performance and microbial composition of a two-stage UASB system treating coffee processing wastewater was assessed. The system was operated with OLR up to 18.2 g COD (L d)-1 and effluent recirculation. Methane production and effluent characteristics were monitored. The microbial composition was examined through next-generation sequencing and qPCR from the anaerobic sludge of the first reactor (R1) operated at low and high OLR. The system showed operational stability, obtaining a maximum methane production of 2.2 L CH4 (L d)-1, with a removal efficiency of COD and phenolic compounds of 84 and 73%, respectively. The performance of R1 at high OLR in steady conditions was associated with an appropriate proportion of nutrients (particularly Fe) and a marked increase of the syntrophic bacteria Syntrophus and Candidatus Cloacimonas, and acetoclastic and hydrogenotrophic methanogens, mainly Methanosaeta, Methanoculleus, Methanobacterium and Methanomassiliicoccus.