The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.

The recent introductions of the bacterium Xylella fastidiosa (Xf) into Europe are linked to the international plant trade. However, both how and when these entries occurred remains poorly understood. Here, we show how almond scorch leaf disease, which affects ~79% of almond trees in Majorca (Spain) and was previously attributed to fungal pathogens, was in fact triggered by the introduction of Xf around 1993 and subsequently spread to grapevines (Pierceʼs disease). We reconstructed the progression of almond leaf scorch disease by using broad phylogenetic evidence supported by epidemiological data. Bayesian phylogenetic inference predicted that both Xf subspecies found in Majorca, fastidiosa ST1 (95% highest posterior density, HPD: 1990–1997) and multiplex ST81 (95% HPD: 1991–1998), shared their most recent common ancestors with Californian Xf populations associated with almonds and grapevines. Consistent with this chronology, Xf-DNA infections were identified in tree rings dating to 1998. Our findings uncover a previously unknown scenario in Europe and reveal how Pierce’s disease reached the continent.

Water used to prepare haemodialysis fluid is not sterile, and its microbiological control is important for the prevention of haemodialysis-associated illness. Bacterial populations inhabiting a distribution system for haemodialysis water were studied over an 18-month period. 203 planktonic bacteria isolated on R2A medium were identified by restriction analysis and sequencing of 16S rRNA gene. A diverse bacterial community was detected, containing predominantly Gram-negative members of the Alphaproteobacteria and Betaproteobacteria, as well as representatives of the genus Mycobacterium. Ecological and clinical consequences are discussed: bacteria from the genera Novosphingobium, Pseudomonas and Sphingomonas have been described in the build-up of biofilms, and others like Acinetobacter, Mycobacterium or Brevibacterium may represent a health risk to patients under haemodialysis treatment.

The horizontal and vertical distribution of representatives of diazotrophic unicellular cyanobacteria was investigated in the subtropical northeast Atlantic Ocean (28.87 to 42.00uN; 9.01 to 20.02uW). Samples from stations encompassing different water conditions (from oceanic oligotrophic waters to upwelling areas and a temperature range of 13.1uC to 24.2uC) were size fractionated and analyzed for nifH by a nested polymerase chain reaction (PCR) and by tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH) using probe Nitro821. In samples from the surface, mixed-layer depth, and deep chlorophyll maximum waters, most (. 50%) of the nifH recovered was from the 0.2-3 mm fraction and was consistent with TSA-FISH counts. The , 3 mm Nitro821-positive cells were more abundant than the larger cells, and the proportion of single cells was larger than that associated with particulate matter or with larger cells. Phylogenetic analysis of representative samples revealed that most of the sequences belong to diazotrophic unicellular cyanobacteria Group A (UCYN-A or Candidatus Atelocyanobacterium thalassa). N 2 fixation in the 0.2-3 mm fraction, putatively representing the activity of UCYN-A, contributed more than 50% of the total N 2 fixation. There was a positive relationship of this putative UCYN-A abundance and activity with temperature, and a negative relationship with dissolved O 2 . The dominance of these putative UCYN-A organisms in nitrate-rich upwelling filament regions suggests that the activity of this group of organisms may not be strongly controlled by the availability of fixed N.

A range of methodologies may be used for analyzing bacteria, depending on the purpose and the level of resolution needed. The capability for recognition of species distinctions within the complex spectrum of bacterial diversity is necessary for progress in microbiological research. In clinical settings, accurate, rapid and cost-effective methods are essential for early and efficient treatment of infections. Characterization and identification of microorganisms, using, bottom-up proteomics, or “proteotyping”, relies on recognition of species-unique or associated peptides, by tandem mass spectrometry analyses, dependent upon an accurate and comprehensive foundation of genome sequence data, allowing for differentiation of species, at amino acid-level resolution. In this study, the high resolution and accuracy of MS/MS-based proteotyping was demonstrated, through analyses of the three phylogenetically and taxonomically most closely-related species of the Mitis Group of the genus Streptococcus: i.e., the pathogenic species, Streptococcus pneumoniae (pneumococcus), and the commensal species, Streptococcus pseudopneumoniae and Streptococcus mitis. To achieve high accuracy, a genome sequence database used for matching peptides was created and carefully curated. Here, MS-based, bottom-up proteotyping was observed and confirmed to attain the level of resolution necessary for differentiating and identifying the most-closely related bacterial species, as demonstrated by analyses of species of the Streptococcus Mitis Group, even when S. pneumoniae were mixed with S. pseudopneumoniae and S. mitis, by matching and identifying more than 200 unique peptides for each species.