RESUMO
Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.
Assuntos
Genoma Bacteriano , Methanomicrobiales/fisiologia , Microbiologia do Solo , Adaptação Fisiológica , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Concentração de Íons de Hidrogênio , Metano/metabolismo , Methanomicrobiales/classificação , Methanomicrobiales/genética , Methanomicrobiales/isolamento & purificação , Metiltransferases/genética , Metiltransferases/metabolismo , Filogenia , Solo/químicaRESUMO
Zymomonas mobilis is an ethanologenic bacterium that has been studied for use in biofuel production. Of the sequenced Zymomonas strains, ATCC 29191 has been described as the phenotypic centrotype of Zymomonas mobilis subsp. mobilis, the taxon that harbors the highest ethanol-producing Z. mobilis strains. ATCC 29191 was isolated in Kinshasa, Congo, from palm wine fermentations. This strain is reported to be a robust levan producer, while in recent years it has been employed in studies addressing Z. mobilis respiration. Here we announce the finishing and annotation of the ATCC 29191 genome, which comprises one chromosome and three plasmids.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Etanol/metabolismo , Genoma Bacteriano , Análise de Sequência de DNA , Zymomonas/genética , Zymomonas/metabolismo , Congo , Fermentação , Frutanos/metabolismo , Redes e Vias Metabólicas , Dados de Sequência Molecular , Oxirredução , Plasmídeos , Vinho/microbiologia , Zymomonas/isolamento & purificaçãoRESUMO
Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65, the type strain of R. aquatilis.
Assuntos
Água Potável/microbiologia , Genoma Bacteriano , Rahnella/genética , Sequência de Bases , França , Dados de Sequência Molecular , Rahnella/classificação , Rahnella/isolamento & purificaçãoRESUMO
Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface soils that is capable of promoting uranium phosphate mineralization as a result of constitutive phosphatase activity. Here we report the first complete genome sequence of an isolate belonging to the genus Rahnella.
Assuntos
Genoma Bacteriano , Metais/química , Radioisótopos/química , Rahnella/genética , Microbiologia do Solo , Sequência de Bases , Dados de Sequência Molecular , Rahnella/classificação , Poluentes do Solo/químicaRESUMO
We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis sp. strain 39116, one of few bacterial species that are known to consume the lignin component of plant biomass. This genome sequence will further ongoing efforts to use microorganisms for the conversion of plant biomass into fuels and high-value chemicals.
Assuntos
Actinobacteria/classificação , Actinobacteria/genética , Biomassa , Genoma Bacteriano , Plantas , Actinobacteria/metabolismo , Biodegradação Ambiental , Cromossomos Bacterianos , DNA Bacteriano/genética , Regulação Bacteriana da Expressão Gênica , Dados de Sequência MolecularRESUMO
Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.
Assuntos
Genoma Bacteriano , Isópteros/microbiologia , Simbiose/fisiologia , Verrucomicrobia/genética , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica/fisiologia , Dados de Sequência MolecularRESUMO
The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
Assuntos
Phytophthora/fisiologia , Doenças das Plantas/microbiologia , Adaptação Fisiológica , Capsicum/microbiologia , Mapeamento Cromossômico , Cucurbita/microbiologia , Regulação da Expressão Gênica , Ligação Genética , Genoma , Genótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients. Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases of pathogen genomes that would ensure more efficient detection, prevention, and control of endemic, emerging, and other infectious disease outbreaks worldwide.
Assuntos
Genômica , Disseminação de Informação , Doenças Transmissíveis/diagnóstico , Bases de Dados Factuais , Saúde Global , Humanos , Internet , Vigilância da PopulaçãoRESUMO
Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.
Assuntos
Bactérias/crescimento & desenvolvimento , Bactérias/genética , Genoma Bacteriano , Ecossistema , Biologia Marinha , Modelos Biológicos , Dados de Sequência Molecular , Photobacterium/genética , Photobacterium/crescimento & desenvolvimento , Sphingomonadaceae/genética , Sphingomonadaceae/crescimento & desenvolvimentoRESUMO
Zymomonas mobilis ATCC 10988 is the type strain of the Z. mobilis subsp. mobilis taxon, members of which are some of the most rigorous ethanol-producing bacteria. Isolated from Agave cactus fermentations in Mexico, ATCC 10988 is one of the first Z. mobilis strains to be described and studied. Its robustness in sucrose-substrate fermentations, physiological characteristics, large number of plasmids, and overall genomic plasticity render this strain important to the study of the species. Here we report the finishing and annotation of the ATCC 10988 chromosomal and plasmid genome.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Zymomonas/genética , Agave/microbiologia , Etanol/metabolismo , Fermentação , Microbiologia de Alimentos , México , Dados de Sequência Molecular , Plasmídeos , Sacarose/metabolismo , Zymomonas/isolamento & purificação , Zymomonas/metabolismo , Zymomonas/fisiologiaRESUMO
Zymomonas mobilis is an alphaproteobacterium studied for bioethanol production. Different strains of this organism have been hitherto sequenced; they all belong to the Z. mobilis subsp. mobilis taxon. Here we report the finished and annotated genome sequence of strain ATCC 29192, a cider-spoiling agent isolated in the United Kingdom. ATCC 29192 is the lectotype of the second-best-characterized subspecies of Z. mobilis, Z. mobilis subsp. pomaceae. The nucleotide sequence of ATCC 29192 deviates from that of Z. mobilis subsp. mobilis representatives, which justifies its distinct taxonomic positioning and proves particularly useful for comparative and functional genomic analyses.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Zymomonas/genética , Etanol/metabolismo , Microbiologia de Alimentos , Dados de Sequência Molecular , Reino Unido , Zymomonas/isolamento & purificação , Zymomonas/metabolismoRESUMO
Glaciecola sp. strain 4H-3-7+YE-5 was isolated from subseafloor sediments at Suruga Bay in Japan and is capable of efficiently hydrolyzing cellulose and xylan. The complete genome sequence of Glaciecola sp. 4H-3-7+YE-5 revealed several genes encoding putatively novel glycoside hydrolases, offering a high potential for plant biomass degradation.
Assuntos
Alteromonadaceae/genética , Alteromonadaceae/isolamento & purificação , Celulose/metabolismo , Genoma Bacteriano , Xilanos/metabolismo , Alteromonadaceae/metabolismo , Biodegradação Ambiental , Sedimentos Geológicos/microbiologia , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Hidrolases/genética , Japão , Dados de Sequência MolecularRESUMO
Streptomyces griseus strain XylebKG-1 is an insect-associated strain of the well-studied actinobacterial species S. griseus. Here, we present the genome of XylebKG-1 and discuss its similarity to the genome of S. griseus subsp. griseus NBRC13350. XylebKG-1 was isolated from the fungus-cultivating Xyleborinus saxesenii system. Given its similarity to free-living S. griseus subsp. griseus NBRC13350, comparative genomics will elucidate critical components of bacterial interactions with insects.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Streptomyces griseus/genética , Animais , Dados de Sequência Molecular , Streptomyces griseus/isolamento & purificação , Gorgulhos/microbiologiaRESUMO
Clostridium thermocellum DSM1313 is a thermophilic, anaerobic bacterium with some of the highest rates of cellulose hydrolysis reported. The complete genome sequence reveals a suite of carbohydrate-active enzymes and demonstrates a level of diversity at the species level distinguishing it from the type strain ATCC 27405.
Assuntos
Clostridium thermocellum/genética , DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Anaerobiose , Celulose/metabolismo , Clostridium thermocellum/metabolismo , Clostridium thermocellum/fisiologia , Temperatura Alta , Dados de Sequência MolecularRESUMO
Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium, which was originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.
Assuntos
Celulose/metabolismo , Genoma Bacteriano , Bacilos Gram-Positivos Formadores de Endosporo/classificação , Bacilos Gram-Positivos Formadores de Endosporo/genética , Celulose/química , Sedimentos Geológicos/microbiologia , Resíduos Industriais , Anotação de Sequência Molecular , Dados de Sequência Molecular , Papel , RNA Bacteriano/genética , Rios , Eliminação de Resíduos Líquidos , Poluentes Químicos da ÁguaRESUMO
Two members of the family Flavobacteriaceae were isolated from subseafloor sediments using artificial seawater with cellulose, xylan, and chitin as the sole carbon and energy sources. Here, we present the complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, which both encode putatively novel enzymes involved in cellulose, hemicellulose, and chitin metabolism.
Assuntos
Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Genoma Bacteriano , Biodegradação Ambiental , Celulose/metabolismo , Quitina/metabolismo , Flavobacteriaceae/enzimologia , Sedimentos Geológicos/microbiologia , Dados de Sequência Molecular , Polissacarídeos/metabolismo , Água do Mar/microbiologiaRESUMO
Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.
Assuntos
Genoma Bacteriano/genética , Ruminococcus/genéticaRESUMO
Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained from root nodules of the American plant Datisca glomerata without isolation in culture.
Assuntos
Frankia/genética , Genoma Bacteriano , Magnoliopsida/microbiologia , Fixação de Nitrogênio , Nódulos Radiculares de Plantas/microbiologia , Sequência de Bases , Frankia/crescimento & desenvolvimento , Frankia/isolamento & purificação , Frankia/fisiologia , Dados de Sequência Molecular , SimbioseRESUMO
Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE's) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).
Assuntos
Bacillales/genética , DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Bacillales/isolamento & purificação , Microbiologia Ambiental , Temperatura Alta , Dados de Sequência MolecularRESUMO
BACKGROUND: Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. RESULTS: With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains. CONCLUSIONS: In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.