Exploring Biodiversity in the Bacterial Community of the Mediterranean Phyllosphere and its Relationship with Airborne Bacteria

We studied the structure and diversity of the phyllosphere bacterial community of a Mediterranean ecosystem, in summer, the most stressful season in this environment. To this aim, we selected nine dominant perennial species, namely Arbutus unedo, Cistus incanus, Lavandula stoechas, Myrtus communis, Phillyrea latifolia, Pistacia lentiscus, Quercus coccifera (woody), Calamintha nepeta, and Melissa officinalis (herbaceous). We also examined the extent to which airborne bacteria resemble the epiphytic ones. Genotype composition of the leaf and airborne bacteria was analysed by using denaturing gradient gel electrophoresis profiling of a 16S rDNA gene fragment; 75 bands were cloned and sequenced corresponding to 28 taxa. Of these, two were found both in the air and the phyllosphere, eight only in the air, and the remaining 18 only in the phyllosphere. Only four taxa were found on leaves of all nine plant species. Cluster analysis showed highest similarity for the five evergreen sclerophyllous species. Aromatic plants were not grouped all together: the representatives of Lamiaceae, bearing both glandular and non-glandular trichomes, formed a separate group, whereas the aromatic and evergreen sclerophyllous M. communis was grouped with the other species of the same habit. The epiphytic communities that were the richest in bacterial taxa were those of C. nepeta and M. officinalis (Lamiaceae). Our results highlight the remarkable presence of lactic acid bacteria in the phyllosphere under the harsh conditions of the Mediterranean summer, the profound dissimilarity in the structure of bacterial communities in phyllosphere and air, and the remarkable differences of leaf microbial communities on neighbouring plants subjected to similar microbial inocula; they also point to the importance of the leaf glandular trichome in determining colonization patterns.     

Novel genetic risk variants for pediatric celiac disease

Background

Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic.

Methods

Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition.

Results

Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G>A, KIAA1109 c.2933T>C and c.4268_4269delCCinsTA, HoxB6 c.668C>A, HoxD12 c.418G>A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n?=?109) and Serbian (n?=?73) descent and their healthy counterparts (n?=?111 and n?=?32, respectively) indicated that HoxD12 c.418G>A is more prevalent in celiac disease patients in the Serbian population (P?<?0.01), while NCK2 c.745_746delAAinsG is less prevalent in celiac disease patients rather than healthy individuals of Greek descent (P?=?0.03). SLC9A4 c.1919G>A and KIAA1109 c.2933T>C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance.

Conclusions

The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology.

     

A flagellar-specific ATPase (FliI) is necessary for flagellar export in Helicobacter pylori

Although flagellar motility is essential for the colonisation of the stomach by Helicobacter pylori, little is known about the regulation of flagellar biosynthesis in this organism. We have identified a gene in H. pylori, designated fliI, whose deduced amino acid sequence revealed extensive homology with the FliI/LcrB/InvC family of proteins which energise the export of flagellar and other virulence factors in several bacterial species. An isogenic mutant of fliI was non-motile and synthesised reduced amounts of flagellin and hook protein subunits. The majority (>99%) of mutant cells were completely aflagellate. These results suggest that FliI is a novel ATPase involved in flagellar export in H. pylori.     

Genome sequences of three Acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78

Acinetobacter baumannii is an emerging opportunistic gram-negative pathogen responsible for hospital-acquired infections. A. baumannii epidemics described in Europe and worldwide were caused by a limited number of genotypic clusters of multidrug-resistant strains. Here, we report the availability of draft genome sequences for three multidrug-resistant A. baumannii strains assigned to multilocus sequence typing genotypes ST2, ST25, and ST78 that were more frequently isolated during outbreaks occurred in Greece, Italy, Lebanon, and Turkey.     

YieJ (CbrC) Mediates CreBC-Dependent Colicin E2 Tolerance in Escherichia coli

Colicin E2-tolerant (known as Cet2) Escherichia coli K-12 mutants overproduce an inner membrane protein, CreD, which is believed to cause the Cet2 phenotype. Here, we show that overproduction of CreD in a Cet2 strain results from hyperactivation of the CreBC two-component regulator, but CreD overproduction is not responsible for the Cet2 phenotype. Through microarray analysis and gene knockout and overexpression studies, we show that overexpression of another CreBC-regulated gene, yieJ (also known as cbrC), causes the Cet2 phenotype.Colicins are protein antibiotics that have various modes of action. They are usually encoded on plasmids and, in many cases, alongside genes encoding colicin immunity factors, which protect colicin-producing cells from the colicin they produce. Of the enzymatic (E) colicins, some carry nuclease activity, including colicin E2, colicin E9, and colicin E3. These three proteins bind to susceptible cells via the surface protein BtuB (the vitamin B₁₂ importer) and, through a series of events that are poorly understood, cross the cell envelope to enter the cytoplasm, where they degrade nucleic acids: colicins E2 and E9 target DNA; colicin E3 targets rRNA (11).Cells can readily become tolerant of E colicins. Mutants usually have lost either the colicin receptor or some protein involved in colicin import. Loss-of-function mutations in btuB confer tolerance of high levels of colicins E2, E9, and E3. Almost 40 years ago, Escherichia coli mutants having a colicin E2-tolerant (Cet2) phenotype were identified. The Cet2 phenotype confers tolerance of colicins E2 and E9 only, while cells remain susceptible to colicin E3, and BtuB is intact (8, 9). Cet2 mutants were shown to overproduce an inner membrane protein (26), and the cet2 mutation was found to be dominant in trans and mapped at 99.9 min on the E. coli chromosome (8, 9). Using the Cet2 mutant RB208 as a source of genomic DNA, a clone able to transform E. coli cells to a Cet2 phenotype was identified. Since this clone carried a gene predicted to encode an inner membrane protein with properties identical to those overproduced in Cet2 mutants, the gene was named cet (15).The cet gene is the last gene in the four-gene cre locus, so cet is also known as creD. The other genes in this locus are creA (hypothetical open reading frame [ORF]); creB, encoding a response regulator; and creC, encoding a sensor kinase. CreB and CreC form a classical two-component regulatory system, and we recently showed that CreBC are activated upon fermentation of glucose in minimal medium or during aerobic growth on minimal medium containing fermentation products, such as pyruvate, lactate, or acetate, as the sole carbon and energy source (10). CreBC controls the expression of a number of genes (the Cre regulon), some of which encode metabolic functions but several of which are hypothetical. One of the most tightly controlled Cre regulon genes is creD (5).We have previously shown that the Cet2 strain RB208 has a point mutation in creC but that creD itself is wild type (5). Since the RB208 genomic clone capable of transforming cells to a Cet2 phenotype carries the whole cre locus, not just creD (15), our hypothesis is that the Cet2 phenotype of the transformant was due to a trans-dominant mutation in the cloned creC mutant allele activating one or more Cre regulon genes and that the Cet2 phenotype may or may not be caused by overexpression of creD. The aims of the experiments described in this paper were to test our hypothesis that the Cet2 phenotype is caused by activating mutations in CreBC and to definitively identify the Cre regulon gene that encodes the colicin E2 tolerance (Cet) protein.     

Plants as Sources of Airborne Bacteria, Including Ice Nucleation-Active Bacteria

Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m³ over young corn and wet soil to 663 colony-forming units per m³ over dry soil and 6,500 colony-forming units per m³ over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.