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July 7, 2019

Genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Cercospora sojina Hara on soybean.

Frogeye leaf spot, caused by Cercospora sojina Hara, is a common disease of soybean in most soybean-growing countries of the world. In this study, we report a high-quality genome sequence of C. sojina by Single Molecule Real-Time sequencing method. The 40.8-Mb genome encodes 11,655 predicated genes, and 8,474 genes are revealed by RNA sequencing. Cercospora sojina genome contains large numbers of gene clusters that are involved in synthesis of secondary metabolites, including mycotoxins and pigments. However, much less carbohydrate-binding module protein encoding genes are identified in C. sojina genome, when compared with other phytopathogenic fungi. Bioinformatics analysis reveals that C. sojina harbours about 752 secreted proteins, and 233 of them are effectors. During early infection, the genes for metabolite biosynthesis and effectors are significantly enriched, suggesting that they may play essential roles in pathogenicity. We further identify 13 effectors that can inhibit BAX-induced cell death. Taken together, our results provide insights into the infection mechanisms of C. sojina on soybean.© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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July 7, 2019

Parallel evolution of group B Streptococcus hypervirulent clonal complex 17 unveils new pathoadaptive mutations.

Group B Streptococcus (GBS) is a commensal of the gastrointestinal and genitourinary tracts, while a prevailing cause of neonatal disease worldwide. Of the various clonal complexes (CCs), CC17 is overrepresented in GBS-infected newborns for reasons that are still largely unknown. Here, we report a comprehensive genomic analysis of 626 CC17 isolates collected worldwide, identifying the genetic traits behind their successful adaptation to humans and the underlying differences between carriage and clinical strains. Comparative analysis with 923 GBS genomes belonging to CC1, CC19, and CC23 revealed that the evolution of CC17 is distinct from that of other human-adapted lineages and recurrently targets functions related to nucleotide and amino acid metabolism, cell adhesion, regulation, and immune evasion. We show that the most distinctive features of disease-specific CC17 isolates were frequent mutations in the virulence-associated CovS and Stk1 kinases, underscoring the crucial role of the entire CovRS regulatory pathway in modulating the pathogenicity of GBS. Importantly, parallel and convergent evolution of major components of the bacterial cell envelope, such as the capsule biosynthesis operon, the pilus, and Rib, reflects adaptation to host immune pressures and should be taken into account in the ongoing development of a GBS vaccine. The presence of recurrent targets of evolution not previously implicated in virulence also opens the way for uncovering new functions involved in host colonization and GBS pathogenesis. IMPORTANCE The incidence of group B Streptococcus (GBS) neonatal disease continues to be a significant cause of concern worldwide. Strains belonging to clonal complex 17 (CC17) are the most frequently responsible for GBS infections in neonates, especially among late-onset disease cases. Therefore, we undertook the largest genomic study of GBS CC17 strains to date to decipher the genetic bases of their remarkable colonization and infection ability. We show that crucial functions involved in different steps of the colonization or infection process of GBS are distinctly mutated during the adaptation of CC17 to the human host. In particular, our results implicate the CovRS two-component regulator of virulence in the differentiation between carriage- and disease-associated isolates. Not only does this work raise important implications for the ongoing development of a vaccine against GBS but might also drive the discovery of key functions for GBS adaptation and pathogenesis that have been overlooked until now. Author Video: An author video summary of this article is available.

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July 7, 2019

A novel aerobic degradation pathway of thiobencarb is initiated by a two-component FMN-dependent monooxygenase system TmoAB in Acidovorax sp. T1.

Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in this strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28-32% identities with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi and dibenzothiophene monooxygenase from Rhodococcus sp.. TmoB shared 25-37% identities with reported flavin reductases and oxidized NADH but not NADPH. TmoAB was an FMN-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD(+) as a cofactor. A gene cluster responsible for complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis.IMPORTANCE Microbial degradation is the main factor of thiobencarb dissipation in soil. In previous reports, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation and dechlorination. However, enzymes and genes involved in microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in strain Acidovorax sp. T1 and identified a novel two-component FMN-dependent monooxygenase system TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical and genetic foundation of thiobencarb degradation in this microorganism. Copyright © 2017 American Society for Microbiology.

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July 7, 2019

Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis.

Shigella flexneri is the primary cause of bacillary dysentery in the developing countries. S. flexneri serotype 1c is a novel serotype, which is found to be endemic in many developing countries, but little is known about its genomic architecture and virulence signatures. We have sequenced for the first time, the complete genome of S. flexneri serotype 1c strain Y394, to provide insights into its diversity and evolution.We generated a high-quality reference genome of S. flexneri serotype 1c using the hybrid methods of long-read single-molecule real-time (SMRT) sequencing technology and short-read MiSeq (Illumina) sequencing technology. The Y394 chromosome is 4.58 Mb in size and shares the basic genomic features with other S. flexneri complete genomes. However, it possesses unique and highly modified O-antigen structure comprising of three distinct O-antigen modifying gene clusters that potentially came from three different bacteriophages. It also possesses a large number of hypothetical unique genes compared to other S. flexneri genomes.Despite a high level of structural and functional similarities of Y394 genome with other S. flexneri genomes, there are marked differences in the pathogenic islands. The diversity in the pathogenic islands suggests that these bacterial pathogens are well adapted to respond to the selection pressures during their evolution, which might contribute to the differences in their virulence potential.

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July 7, 2019

Population structure and local adaptation of MAC lung disease agent Mycobacterium avium subsp. hominissuis.

Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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July 7, 2019

Metagenome-assembled genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 from a cathode-associated acetogenic microbial community.

Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 were obtained from the metagenome of a cathode-associated community enriched within a microbial electrosynthesis system (MES). The draft genome sequences provide insight into the functional potential of these microorganisms within an MES and a foundation for future comparative analyses. Copyright © 2017 Ross et al.

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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

Parallel evolution of two clades of a major Atlantic endemic Vibrio parahaemolyticus pathogen lineage by independent acquisition of related pathogenicity islands.

Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased from locations with historically low disease incidence, such as the Northeast United States (US). This change coincided with a bacterial population shift towards human pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43 and ST636) to near-shore areas off the Atlantic coast of the Northeast US. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human pathogenic variant evolved independently through acquisition of distinct Vibrio pathogenicity islands (VPaI). These VPaI differ from each other and bear little resemblance to hemolysin-containing VPaI from isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored no hemolysins, or contained a chromosome I-inserted island we call VPaIß that encodes a type three secretion system (T3SS2ß) typical of Trh hemolysin-producers. The more clinically prevalent and clonal ST631 clade II had an island we call VPaI? that encodes both tdh and trh and that was inserted in chromosome II. VPaI? was derived from VPaIß but with some additional acquired elements in common with VPaI carried by pandemic isolates, exemplifying the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon assays identified VPaI?-type islands containing tdh inserted adjacent to the ure cluster in the three introduced Pacific and most other emergent lineages. that collectively cause 67% of Northeast US infections as of 2016.IMPORTANCE The availability of three different hemolysin genotypes in the ST631 lineage provided a unique opportunity to employ genome comparisons to further our understanding of the processes underlying pathogen evolution. The fact that two different pathogenic clades arose in parallel from the same potentially benign lineage by independent VPaI acquisition is surprising considering the historically low prevalence of community members harboring VPaI in waters along the Northeast US coast that could serve as the source of this material. This illustrates a possible predisposition of some lineages to not only acquire foreign DNA but also to become human pathogens. Whereas the underlying cause for the expansion of V. parahaemolyticus lineages harboring VPaI? along the US Atlantic coast and spread of this element to multiple lineages that underlies disease emergence is not known, this work underscores the need to define the environment factors that favor bacteria harboring VPaI in locations of emergent disease. Copyright © 2017 American Society for Microbiology.

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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

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

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

Complete genome sequence of the fruiting myxobacterium Myxococcus macrosporus strain DSM 14697, generated by PacBio sequencing.

Members of the Myxococcales order initiate a developmental program in response to starvation that culminates in formation of spore-filled fruiting bodies. To investigate the genetic basis for fruiting body formation, we present the complete 8.9-Mb genome sequence of Myxococcus macrosporus strain DSM 14697, generated using the PacBio sequencing platform. Copyright © 2017 Treuner-Lange et al.

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