We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is multiresistant to antibiotics. We first sequenced gyrA, gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found that PA7 is a taxonomic outlier. We report here the complete sequence of the 6,588,339 bp genome, which has only about 95% overall identity to other strains. PA7 has multiple novel genomic islands and a total of 51 occupied regions of genomic plasticity. These islands include antibiotic resistance genes, parts of transposons, prophages, and a pKLC102-related island. Several PA7 genes not present in PAO1 or PA14 are putative orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7 appears to be closely related to the known taxonomic outlier DSM1128 (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin type II. Preliminary proteomic studies indicate numerous differences with PAO1, some of which are probably a consequence of a frameshift mutation in the mvfR quorum sensing regulatory gene.

The GacS/GacA signal transduction system is a central regulator in Pseudomonas spp., including the biological control strain P. fluorescens Pf-5, in which GacS/GacA controls the production of secondary metabolites and exoenzymes that suppress plant pathogens. A whole genome oligonucleotide microarray was developed for Pf-5 and used to assess the global transcriptomic consequences of a gacA mutation in P. fluorescens Pf-5. In cultures at the transition from exponential to stationary growth phase, GacA significantly influenced transcript levels of 635 genes, representing more than 10% of the 6147 annotated genes in the Pf-5 genome. Transcripts of genes involved in the production of hydrogen cyanide, the antibiotic pyoluteorin and the extracellular protease AprA were at a low level in the gacA mutant, whereas those functioning in siderophore production and other aspects of iron homeostasis were significantly higher in the gacA mutant than in wild-type Pf-5. Notable effects of gacA inactivation were also observed in the transcription of genes encoding components of a type VI secretion system and cytochrome c oxidase subunits. Two novel gene clusters expressed under the control of gacA were identified from transcriptome analysis, and we propose global-regulator-based genome mining as an approach to decipher the secondary metabolome of Pseudomonas spp.

Thermostable enzymes and thermophilic cell factories may afford economic advantages inFurthermore, we present evidence suggesting that aside from representing a potential 9 reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using 10 classical and molecular genetics. 11Rapid, efficient and robust enzymatic degradation of biomass-derived polysaccharides is 12 currently a major challenge for biofuel production. A prerequisite is the availability of enzymes 13 that hydrolyze cellulose, hemicellulose and other polysaccharides into fermentable sugars at 14 conditions suitable for industrial use. The best studied and most widely used cellulases and to overcome these obstacles is to raise the reaction temperature, thereby increasing hydrolytic 20 rates and reducing contamination risks. AT-rich repetitive regions (Fig. 1) To examine the strategy used by these thermophiles for decomposition of plant cell wall 9 polysaccharides, we used RNA-Seq to compare transcript profiles during growth on barley straw 10 or alfalfa straw to growth on glucose. Alfalfa was chosen to represent dicotyledonous plants, 11 whereas barley was used to represent monocotyledon plants. The major difference between these 12 materials is that the carbohydrates from barley cell wall are mainly cellulose and hemicellulose 13 with a negligible amount of pectin 11 , whereas alfalfa cell wall contains pectin and xylan in 14 roughly similar proportions, each consisting of 15-20% of total carbohydrates 12, . 15 We observed notable differences between the transcriptional profiles of genes encoding conditions. For example, the orthologs in Clades A, B, E, G and P of GH61 are upregulated 8 under growth in complex substrates for both thermophiles (Fig. 2b). An even more striking 9 correlation between transcript levels and orthologs is evident for the GH6 and GH7 cellulases 10 ( Supplementary Fig. 7) where the transcript profiles for the orthologs of the two organisms are Table 7). Thermophilic fungi are major components of the microflora in self-heating composts. They 9 break down cellulose at a faster rate than prodigious, mesophilic cellulase producers such as T. Tables 11-14). On the basis of 24 our comparative analyses of the genomes from two thermophilic fungi, we conclude that their 25 nucleotide and protein features are different from those observed in thermophilic prokaryotes. 26 We also investigated the possibility that thermophilic fungi possess major differences in 27 processes mediating thermophily including heat shock, oxidative stress, membrane biosynthesis, 28 chromatin structure and modification, and fungal cell wall metabolism. We compared the 29 proteins predicted to be involved in these processes in C. globosum, M. thermophila and T. 30 terrestris, but were unable to find differences that can convincingly be interpreted as the Fig. 9). Within the Sordiariales, thermophily 6 is restricted to subgroups of the family Chaetomiaceae. Among fungi more broadly, thermophily 7 also exists in the Zygomycota, but it ...

Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.

All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.

Plastic pollution is a global threat to marine ecosystems. Plastic litter can leach a variety of substances into marine environments; however, virtually nothing is known regarding how this affects photosynthetic bacteria at the base of the marine food web. To address this, we investigated the effect of plastic leachate exposure on marine Prochlorococcus , widely considered the most abundant photosynthetic organism on Earth and vital contributors to global primary production and carbon cycling. Two strains of Prochlorococcus representing distinct ecotypes were exposed to leachate from common plastic items: high-density polyethylene bags and polyvinyl chloride matting. We show leachate exposure strongly impairs Prochlorococcus in vitro growth and photosynthetic capacity and results in genome-wide transcriptional changes. The strains showed distinct differences in the extent and timing of their response to each leachate. Consequently, plastic leachate exposure could influence marine Prochlorococcus community composition and potentially the broader composition and productivity of ocean phytoplankton communities.

bAcinetobacter baumannii has become a major problem in the clinical setting with the prevalence of infections caused by multidrug-resistant strains on the increase. Nevertheless, only a limited number of molecular mechanisms involved in the success of A. baumannii as a human pathogen have been described. In this study, we examined the virulence features of a hypermotile derivative of A. baumannii strain ATCC 17978, which was found to display enhanced adherence to human pneumocytes and elevated levels of lethality toward Caenorhabditis elegans nematodes. Analysis of cellular lipids revealed modifications to the fatty acid composition, providing a possible explanation for the observed changes in hydrophobicity and subsequent alteration in adherence and motility. Comparison of the genome sequences of the hypermotile variant and parental strain revealed that an insertion sequence had disrupted an hns-like gene in the variant. This gene encodes a homologue of the histone-like nucleoid structuring (H-NS) protein, a known global transcriptional repressor. Transcriptome analysis identified the global effects of this mutation on gene expression, with major changes seen in the autotransporter Ata, a type VI secretion system, and a type I pilus cluster. Interestingly, isolation and analysis of a second independent hypermotile ATCC 17978 variant revealed a mutation to a residue within the DNA binding region of H-NS. Taken together, these mutants indicate that the phenotypic and transcriptomic differences seen are due to loss of regulatory control effected by H-NS.