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July 7, 2019

Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition.

Most land plants live in association with arbuscular mycorrhizal (AM) fungi and rely on this symbiosis to scavenge phosphorus (P) from soil. The ability to establish this partnership has been lost in some plant lineages like the Brassicaceae, which raises the question of what alternative nutrition strategies such plants have to grow in P-impoverished soils. To understand the contribution of plant-microbiota interactions, we studied the root-associated fungal microbiome of Arabis alpina (Brassicaceae) with the hypothesis that some of its components can promote plant P acquisition. Using amplicon sequencing of the fungal internal transcribed spacer 2, we studied the root and rhizosphere fungal communities of A. alpina growing under natural and controlled conditions including low-P soils and identified a set of 15 fungal taxa consistently detected in its roots. This cohort included a Helotiales taxon exhibiting high abundance in roots of wild A. alpina growing in an extremely P-limited soil. Consequently, we isolated and subsequently reintroduced a specimen from this taxon into its native P-poor soil in which it improved plant growth and P uptake. The fungus exhibited mycorrhiza-like traits including colonization of the root endosphere and P transfer to the plant. Genome analysis revealed a link between its endophytic lifestyle and the expansion of its repertoire of carbohydrate-active enzymes. We report the discovery of a plant-fungus interaction facilitating the growth of a nonmycorrhizal plant under native P-limited conditions, thus uncovering a previously underestimated role of root fungal microbiota in P cycling.

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July 7, 2019

First complete genome sequences of Xanthomonas citri pv. vignicola strains CFBP7111, CFBP7112, and CFBP7113 obtained using long-read technology

Xanthomonas citri pv. vignicola strains cause bacterial blight of the legume crop cowpea. We report whole-genome sequences of three X. citri pv. vignicola strains obtained using PacBio single-molecule real-time sequencing. Such genomic data provide new information on pathogenicity factors, such as transcription activator-like effectors. Copyright © 2017 Ruh et al.

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July 7, 2019

Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.

Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-µm-long adhesin using a “dissect and build” structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises ~120 identical immunoglobulin-like ß-sandwich domains that rigidify on binding Ca(2+) to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several “repeats-in-toxin” motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.

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July 7, 2019

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale.

Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin-resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC™ 9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E. hirae R17. The functions of these R17 strain-specific coding sequences relate to the COGs categories of carbohydrate transport and metabolism and transcription, a finding that suggests the carbohydrate utilization capacity of E. hirae R17 may be more extensive when compared with the other three bacterial species (spp.). Analysis of genomic islands and virulence genes highlighted the potential that horizontal gene transfer played as a contributor of variations in pathogenicity in this isolate. Drug-resistance gene prediction and antibiotic susceptibility testing indicated E. hirae R17 was resistant to several antimicrobial compounds, including bacitracin, ciprofloxacin, daptomycin, erythromycin, and tetracycline, thereby limiting chemotherapeutic treatment options. Further, tolerance to biocides and metals may confer a phenotype that facilitates the survival and adaptation of this isolate against food preservatives, disinfectants, and antibacterial coatings. The genomic plasticity, mediated by IS elements, transposases, and tandem repeats, identified in the E. hirae R17 genome may support adaptation to new environmental niches, such as those that are found in hospitalized patients. A predicted transmissible plasmid, pRZ1, was found to carry several antimicrobial determinants, along with some predicted pathogenic genes. These data supported the previously determined phenotype confirming that the foodborne E. hirae R17 is a multidrug-resistant pathogenic bacterium with evident genome plasticity and environmental adaptability.© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

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July 7, 2019

Complete genome sequence of Ralstonia solanacearum FJAT-91, a high-virulence pathogen of tomato wilt.

Ralstonia solanacearum FJAT-91, which displays higher virulence toward plants belonging to the family Solanaceae, was isolated from a wilted tomato plant vessel in Fujian province, southeast China. Here, we report the complete genome sequence of R. solanacearum FJAT-91 using long-read single-molecule PacBio sequencing technology. The genome comprises a 3,873,214-bp circular chromosome and a 2,000,873-bp circular megaplasmid with an overall G+C content of 66.85%. Copyright © 2017 Chen et al.

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July 7, 2019

Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup.

Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs). PSGs are almost exclusively expressed by trophoblast cells at the maternal-fetal interface. The reason why PSGs exist only in a minority of mammals is still unknown.Analysis of the CEA gene family in bats revealed that in certain bat families, belonging to the subgroup Yangochiroptera but not the Yinpterochiroptera subgroup an expansion of the CEA gene family took place, resulting in approximately one hundred CEA family genes in some species of the Vespertilionidae. The majority of these genes encode secreted PSG-like proteins (further referred to as PSG). Remarkably, we found strong evidence that the ligand-binding domain (IgV-like domain) of PSG is under diversifying positive selection indicating that bat PSGs may interact with structurally highly variable ligands. Such ligands might represent bacterial or viral pathogen adhesins. We have identified two distinct clusters of PSGs in three Myotis species. The two PSG cluster differ in the amino acids under positive selection. One cluster was only expanded in members of the Vespertilionidae while the other was found to be expanded in addition in members of the Miniopteridae and Mormoopidae. Thus one round of PSG expansion may have occurred in an ancestry of all three families and a second only in Vespertilionidae. Although maternal ligands of PSGs may exist selective challenges by two distinct pathogens seem to be likely responsible for the expansion of PSGs in Vespertilionidae.The rapid expansion of PSGs in certain bat species together with selection for diversification suggest that bat PSGs could be part of a pathogen defense system by serving as decoy receptors and/or regulators of feto-maternal interactions.

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July 7, 2019

Draft genome sequence of the plant pathogen Streptomyces sp. strain 11-1-2.

Streptomyces sp. strain 11-1-2 is a Gram-positive filamentous bacterium that was isolated from a common scab lesion on a potato tuber. The strain is highly pathogenic to plants but does not produce the virulence-associated Streptomyces phytotoxin thaxtomin A. Here, we report the draft genome sequence of Streptomyces sp. 11-1-2. Copyright © 2017 Bown and Bignell.

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July 7, 2019

Key features of mcr-1-bearing plasmids from Escherichia coli isolated from humans and food.

Mcr-1-harboring Enterobacteriaceae are reported worldwide since their first discovery in 2015. However, a limited number of studies are available that compared full-length plasmid sequences of human and animal origins.In this study, mcr-1-bearing plasmids from seven Escherichia coli isolates recovered from patients (n = 3), poultry meat (n = 2) and turkey meat (n = 2) in Switzerland were further analyzed and compared. Isolates were characterized by multilocus sequence typing (MLST). The mcr-1-bearing plasmids were transferred by transformation into reference strain E. coli DH5a and MCR-1-producing transformants were selected on LB-agar supplemented with 2 mg/L colistin. Purified plasmids were then sequenced and compared.MLST revealed six distinct STs, illustrating the high clonal diversity among mcr-1-positive E. coli isolates of different origins. Two different mcr-1-positive plasmids were identified from a single E. coli ST48 human isolate. All other isolates possessed a single mcr-1 harboring plasmid. Transferable IncI2 (size ca. 60-61 kb) and IncX4 (size ca. 33-35 kb) type plasmids each bearing mcr-1 were found associated with human and food isolates. None of the mcr-1-positive IncI2 and IncX4 plasmids possessed any additional resistance determinants. Surprisingly, all but one of the sequenced mcr-1-positive plasmids lacked the ISApl1 element, which is a key element mediating acquisition of mcr-1 into various plasmid backbones.There is strong evidence that the food chain may be an important transmission route for mcr-1-bearing plasmids. Our data suggest that some “epidemic” plasmids rather than specific E. coli clones might be responsible for the spread of the mcr-1 gene along the food chain.

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July 7, 2019

Convergent evolution of Y chromosome gene content in flies.

Sex-chromosomes have formed repeatedly across Diptera from ordinary autosomes, and X-chromosomes mostly conserve their ancestral genes. Y-chromosomes are characterized by abundant gene-loss and an accumulation of repetitive DNA, yet the nature of the gene repertoire of fly Y-chromosomes is largely unknown. Here we trace gene-content evolution of Y-chromosomes across 22 Diptera species, using a subtraction pipeline that infers Y genes from male and female genome, and transcriptome data. Few genes remain on old Y-chromosomes, but the number of inferred Y-genes varies substantially between species. Young Y-chromosomes still show clear evidence of their autosomal origins, but most genes on old Y-chromosomes are not simply remnants of genes originally present on the proto-sex-chromosome that escaped degeneration, but instead were recruited secondarily from autosomes. Despite almost no overlap in Y-linked gene content in different species with independently formed sex-chromosomes, we find that Y-linked genes have evolved convergent gene functions associated with testis expression. Thus, male-specific selection appears as a dominant force shaping gene-content evolution of Y-chromosomes across fly species.While X-chromosome gene content tends to be conserved, Y-chromosome evolution is dynamic and difficult to reconstruct. Here, Mahajan and Bachtrog use a subtraction pipeline to identify Y-linked genes in 22 Diptera species, revealing patterns of Y-chromosome gene-content evolution.

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July 7, 2019

The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence.

Pseudomonas aeruginosa is an opportunistic pathogen that causes severe airway infections in humans. These infections are usually difficult to treat and associated with high mortality rates. While colonizing the human airways, P. aeruginosa could accumulate genetic mutations that often lead to its better adaptability to the host environment. Understanding these evolutionary traits may provide important clues for the development of effective therapies to treat P. aeruginosa infections. In this study, 25 P. aeruginosa isolates were longitudinally sampled from the airways of four ventilator-associated pneumonia (VAP) patients. Pacbio and Illumina sequencing were used to analyse the in vivo evolutionary trajectories of these isolates. Our analysis showed that positive selection dominantly shaped P. aeruginosa genomes during VAP infections and led to three convergent evolution events, including loss-of-function mutations of lasR and mpl, and a pyoverdine-deficient phenotype. Specifically, lasR encodes one of the major transcriptional regulators in quorum sensing, whereas mpl encodes an enzyme responsible for recycling cell wall peptidoglycan. We also found that P. aeruginosa isolated at late stages of VAP infections produce less elastase and are less virulent in vivo than their earlier isolated counterparts, suggesting the short-term in vivo evolution of P. aeruginosa leads to attenuated virulence.© 2017 The Authors.

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July 7, 2019

Complete genome sequence of Mycoplasma hyopneumoniae strain KM014, a clinical isolate from South Korea.

Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia, resulting in considerable economic losses in the swine industry. A few genome sequences of M. hyopneumoniae have been reported to date, implying that additional genome data are needed for further genetic studies. Here, we present the annotated genome sequence of M. hyopneumoniae strain KM014. Copyright © 2017 Han et al.

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July 7, 2019

Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis.

Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of A. alpinus strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes.

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July 7, 2019

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length?>2.6?Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes.© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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