Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate.

Pseudomonas aeruginosa is a widespread γ-proteobacterium and an important opportunistic pathogen. The genetically diverse P. aeruginosa phylogroup 3 strains are characterized by producing the pore-forming ExlA toxin and by their lack of a type III secretion system. However, like all strains of this species, they produce several virulence-associated traits, such as elastase, rhamnolipids and pyocyanin, which are regulated by quorum sensing (QS). The P. aeruginosa QS response comprises three systems (Las, Rhl and Pqs, respectively) that hierarchically regulate these virulence factors. The Pqs QS system is composed of the PqsR transcriptional factor, which, coupled with the alkyl-quinolones HHQ or PQS, activates the transcription of the pqsABCDE operon. The products of the first four genes of this operon produce HHQ, which is then converted to PQS by PqsH, while PqsE forms a complex with RhlR and stabilizes it. In this study we report that mutations affecting the Pqs system are particularly common in phylogroup 3 strains. To better understand QS in phylogroup 3 strains we studied strain MAZ105 isolated from tomato rhizosphere and showed that it contains mutations in the central QS transcriptional regulator, LasR, and in the gene encoding the PqsA enzyme involved in the synthesis of PQS. However, it can still produce QS-regulated virulence factors and is virulent in Galleria mellonella and mildly pathogenic in the mouse abscess/necrosis model; our results show that this may be due to the expression of pqsE from a different PqsR-independent promoter than the pqsA promoter. Our results indicate that using anti-virulence therapy based on targeting the PQS system will not be effective against infections by P. aeruginosa phylogroup 3 strains.

Involvement of cyclodipeptides in the competition of bacterial communities in the oligotrophic Churince aquatic system of Cuatro Ciénegas Basin dominated by Gammaproteobacteria.

The Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert in México is an extremely oligotrophic oasis with negligible phosphorous levels, described as a hot spot of biodiversity, not only in stromatolites and microbial mats, but also in living forms in general. The microorganisms possess the capability to produce a wide variety of virulence factors, antibiotics, and quorum-sensing (QS) crosstalk signals such as non-ribosomal cyclodipeptides (CDPs) which enables them to colonize diverse ecological niches. In the aquatic system of CCB known as Churince, a bacterial population was isolated from the Lagunita pond dominated by Gammaproteobacteria. In this work, we determined the relationships between the antagonism and CDPs production in this bacterial population. Results indicate that 68% of isolates showed antagonistic effects over other isolates, correlating with production of CDPs and the antibiotic 2,4-diacetylphloroglucinol (DAPG). Although a minority of the isolates were capable of inducing a QS biosensor strain, bacterial QS interference was not the main mechanism in the antagonism observed. Thus, our results indicate that CDPs primarily, and DAPG to a lesser degree, are involved with the growth-inhibition competition mechanisms of bacterial communities in the Lagunita pond and was associated with a Gammaproteobacteria dominancy phenomena.

Crop genetic diversity uncovers metabolites, elements, and gene networks predicted to be associated with high plant biomass yields in maize.

Rapid population growth and increasing demand for food, feed, and bioenergy in these times of unprecedented climate change require breeding for increased biomass production on the world's croplands. To accelerate breeding programs, knowledge of the relationship between biomass features and underlying gene networks is needed to guide future breeding efforts. To this end, large-scale multiomics datasets were created with genetically diverse maize lines, all grown in long-term organic and conventional cropping systems. Analysis of the datasets, integrated using regression modeling and network analysis revealed key metabolites, elements, gene transcripts, and gene networks, whose contents during vegetative growth substantially influence the build-up of plant biomass in the reproductive phase. We found that S and P content in the source leaf and P content in the root during the vegetative stage contributed the most to predicting plant performance at the reproductive stage. In agreement with the Gene Ontology enrichment analysis, the cis-motifs and identified transcription factors associated with upregulated genes under phosphate deficiency showed great diversity in the molecular response to phosphate deficiency in selected lines. Furthermore, our data demonstrate that genotype-dependent uptake, assimilation, and allocation of essential nutrient elements (especially C and N) during vegetative growth under phosphate starvation plays an important role in determining plant biomass by controlling root traits related to nutrient uptake. These integrative multiomics results revealed key factors underlying maize productivity and open new opportunities for efficient, rapid, and cost-effective plant breeding to increase biomass yield of the cereal crop maize under adverse environmental factors.

MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.

Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.

The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally.

One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3'-5'-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species. This work is not intended to give an exhaustive revision of bacterial CRP-orthologs, but to provide examples of the role that these proteins play in the expression of genes that are fundamental for the life style of some bacterial species. We highlight the conservation of their structural characteristics and of their binding to conserved-DNA sequences, in contrast to their very diverse repertoire of gene activation. CRP activates a wide variety of fundamental genes for the biological characteristic of each bacterial species, which in several instances form part of their core-genome (defined as the gene sequences present in all members of a bacterial species). We present evidence that support the fact that some of the transcriptional regulators that belong to the CRP family in different bacterial species, and some of the genes that are regulated by them, can be inherited by horizontal gene transfer. These data are discussed in the framework of bacterial evolution models.

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment.

The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after 3 weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition.