RESUMEN
Thalassospira sp. SW-3-3 is a bacterial strain isolated from deep seawater of the Pacific Ocean at a water depth of 3112 m. It is a Gram-negative, aerobic, and curved rod-shaped bacterium belonging to the family Thalassospiraceae. In this study, we report the complete genome sequence of strain SW-3-3. It has a circular chromosome with a size of 4,764,478 bp and a G + C content of 54.7%. The genome contains 4296 protein-coding genes, 63 tRNA genes, and 12 rRNA genes. Genomic analysis shows that strain SW-3-3 contains genes and catalytic pathways relevant to phthalate metabolism. Phthalates are well-known emerging contaminants that are harmful to environments and human health. They are chemically stable compounds that are widely used in plastic products and are pervasive in our life. With the discharge of plastic pollutants, a huge number of phthalate compounds enter the ocean. The genetic information of strain SW-3-3 suggests that it has the potential to metabolize phthalates. There are 9 key enzymes in the metabolization pathway, and phthalates are finally catalyzed to produce succinyl-CoA which is further degraded through the tricarboxylic acid (TCA) cycle pathway. This genomic analysis will be helpful for further understanding of the applications of strain SW-3-3 in the remediation of phthalate pollution.
Asunto(s)
Restauración y Remediación Ambiental , Rhodospirillaceae , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Genómica , Humanos , Ácidos Ftálicos , Filogenia , Plásticos , ARN Ribosómico 16S/genética , Rhodospirillaceae/genética , Agua de Mar/microbiología , Análisis de Secuencia de ADNRESUMEN
An ectoine-producing bacterium, designated SWCN16T, was isolated from seawater and could be grown in a medium containing up to 12 % NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SWCN16T belonged to the genus Aestuariispira, class Alphaproteobacteria, and shared the highest 16S rRNA gene sequence similarity of 96.8% with Aestuariispira insulae CECT 8488T. The phenotypic, chemotaxonomic, and genotypic characteristics findings of this study suggested that strain SWCN16T represented a novel species of the genus Aestuariispira. We propose the name Aestuariispira ectoiniformans sp. nov. for this species. Whole-genome sequencing analysis of the isolate revealed a putative ectABC gene cluster for ectoine biosynthesis. These genes were found to be functional using ectoine synthesis testing and S16-ectBAC cells, which were pET21a-ectBAC-transformed E. coli BL21 cells. We found that S16-ectBAC synthesized about 1.67 g/L extracellular ectoine and about 0.59 g/L intracellular ectoine via bioconversion at optimum conditions.
Asunto(s)
Aminoácidos Diaminos , Rhodospirillaceae , Agua de Mar , Aminoácidos Diaminos/genética , Escherichia coli/genética , Genes Bacterianos/genética , Familia de Multigenes , Filogenia , ARN Ribosómico 16S/genética , Rhodospirillaceae/clasificación , Rhodospirillaceae/genética , Agua de Mar/microbiología , Especificidad de la EspecieRESUMEN
Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. IMPORTANCE The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of Thalassospira that have accumulated mutations in their genomes over millions of years.
Asunto(s)
Evolución Molecular , Genoma Bacteriano , Sedimentos Geológicos/microbiología , Mutación Puntual , Rhodospirillaceae/genética , Variación Genética , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Factores de TiempoRESUMEN
Energy crisis and global climate change have driven an increased effort toward biofuel synthesis from renewable feedstocks. Herein, purple nonsulfur photosynthetic bacterium (PNSB) of Rhodobacter capsulatus was explored as a platform for high-titer production of a terpene-based advanced biofuel-bisabolene. A multilevel engineering strategy such as promoter screening, improving the NADPH availability, strengthening the precursor supply, suppressing the side pathways, and introducing a heterologous mevalonate pathway, was used to improve the bisabolene titer in R. capsulatus. The above strategies enabled a 35-fold higher titer of bisabolene than that of the starting strain, reaching 1089.7 mg/L from glucose in a shake flask. The engineered strain produced 9.8 g/L bisabolene with a yield of >0.196 g/g-glucose under the two-phase fed-batch fermentation, which corresponds to >78% of theoretical maximum. Taken together, our work represents one of the pioneering studies to demonstrate PNSB as a promising platform for terpene-based advanced biofuel production.
Asunto(s)
Biocombustibles , Ingeniería Metabólica/métodos , Rhodobacter capsulatus/metabolismo , Rhodospirillaceae/metabolismo , Terpenos/metabolismo , Técnicas de Cultivo Celular por Lotes/métodos , Sistemas CRISPR-Cas , Escherichia coli/genética , Fermentación , Edición Génica/métodos , Glucosa/metabolismo , Ácido Mevalónico/metabolismo , NADP/genética , NADP/metabolismo , Fotosíntesis , Regiones Promotoras Genéticas/genética , Rhodobacter capsulatus/genética , Rhodospirillaceae/genéticaRESUMEN
Marine purple photosynthetic bacteria are ideal organisms for the production of useful materials at reduced costs and contributing to a sustainable society because they can utilize sunlight, seawater, and components of air, including carbon dioxide and nitrogen gases, for their growth. However, conjugation is the only applicable method for the transformation of marine purple photosynthetic bacteria so far. Here, we examined a calcium chloride-mediated method for the transformation of marine purple photosynthetic bacteria. Plasmid DNAs containing the kanamycin resistance gene were successfully transferred into chemically competent cells of two strains of marine purple photosynthetic bacteria (Rhodovulum sulfidophilum and Roseospira marina). Heat shock treatment increased the transformation efficiency in R. sulfidophilum, whereas the addition of cell-penetrating peptide did not improve it. We also found that prolonged incubation in agar plates containing kanamycin led to spontaneous mutation of the 16S rRNA, resulting in kanamycin resistance in R. marina. Thus, we developed an efficient and facile transformation method using chemically competent cells of marine purple photosynthetic bacteria with calcium chloride.
Asunto(s)
Técnicas de Transferencia de Gen , Resistencia a la Kanamicina/genética , Rhodospirillaceae/genética , Rhodovulum/genética , Transformación Bacteriana/genética , Cloruro de Calcio/química , ADN Bacteriano/química , ADN Bacteriano/genética , Respuesta al Choque Térmico/fisiología , Plásmidos/genética , Agua de Mar/microbiología , Microbiología del AguaRESUMEN
Metal whole-cell biosensors (WCBs) have been reported as very useful tools to detect and quantify the presence of bioavailable fractions of certain metals in water and soil samples. In the current work, two bacterial WCBs able to report Cr(VI) presence and plants growing on Cr(VI)-enriched soil/medium were used to assess the potential transfer of this metal to organisms of higher trophic levels, and the risk of transfer to the food chain. To do it, the functionality of the WCBs within tissues of inoculated plants in contact with Cr(VI)-contaminated soil and water was studied in vitro and in a controlled greenhouse environment. One WCB was the previously described Ochrobactrum tritici pCHRGFP2 and the second, Nitrospirillum amazonense pCHRGFP2, is a newly engineered naturally-occurring endophytic microorganism. Three rice varieties (IAC 4440, BRS 6 CHUÍ, IRGA 425) and one maize variety (1060) were tested as hosts and subjected to Cr(VI) treatments (25 µM), with different results obtained. Inoculation of each WCB into plants exposed to Cr(VI) showed GFP expression within plant tissues. WCBs penetrated the root tissues and later colonized the shoots and leaves. In general, a higher fluorescence signal was detected in roots, together with a higher Cr content and denser WCB colonization. Best fluorescence intensities per plant biomass of shoots were obtained for plant host IRGA 425. Therefore, by analyzing colonized tissues, both WCBs allowed the detection of Cr(VI) contamination in soils and its transfer to plants commonly used in crops for human diet.
Asunto(s)
Técnicas Biosensibles/métodos , Cromo/análisis , Ochrobactrum/crecimiento & desarrollo , Oryza/química , Rhodospirillaceae/crecimiento & desarrollo , Zea mays/química , Disponibilidad Biológica , Ingeniería Metabólica , Microscopía Fluorescente , Ochrobactrum/genética , Ochrobactrum/metabolismo , Oryza/crecimiento & desarrollo , Oryza/microbiología , Rhodospirillaceae/genética , Rhodospirillaceae/metabolismo , Contaminantes del Suelo/análisis , Contaminantes Químicos del Agua/análisis , Zea mays/crecimiento & desarrollo , Zea mays/microbiologíaRESUMEN
Rhodospirillaceae represents a major family of the class alphaproteobacteria that includes an increasing number of functionally diverse taxa. The aim of this work is to evaluate the present phylogenetic diversity of the Rhodospirillaceae, which includes several metagenome-assembled genomes of uncultivated bacteria, as well as cultivated bacteria that were previously classified in different families. Various methodological approaches have been followed to discern the phylogenetic diversity of the taxa associated with the Rhodospirillaceae, which are grouped in three major sub-divisions and several other taxonomic entities that are currently confined to the genus rank. These genera include Tistrella, Elstera, Dongia and Ferrovibrio among cultivated organisms and alphaproteobacteria bacterium 41-28 among uncultivated bacteria. Overall, this study adds at least 11 genera and over 40 species to the current set of taxa belonging to the Rhodospirillaceae, a taxonomic term that clearly requires amendment. We propose to re-classify all taxa associated with the Rhodospirillaceae family under the new order, Diaforabacterales ord. nov. (from the Greek word for diversity, διάφορα). This study also uncovers the likely root of Rhodospirillaceae among recently reported metagenome-assembled genomes of uncultivated marine and groundwater bacteria.
Asunto(s)
Rhodospirillaceae/clasificación , Proteínas Bacterianas/genética , Filogenia , Rhodospirillaceae/genética , Proteínas Ribosómicas/genéticaAsunto(s)
Infecciones por Bacterias Gramnegativas/diagnóstico , Mastoiditis/microbiología , Rhodospirillaceae/aislamiento & purificación , Anciano , Antibacterianos/uso terapéutico , Técnicas Bacteriológicas , Infecciones por Bacterias Gramnegativas/líquido cefalorraquídeo , Infecciones por Bacterias Gramnegativas/tratamiento farmacológico , Infecciones por Bacterias Gramnegativas/microbiología , Humanos , Masculino , Mastoiditis/líquido cefalorraquídeo , Mastoiditis/diagnóstico por imagen , Mastoiditis/tratamiento farmacológico , Técnicas de Diagnóstico Molecular , ARN Ribosómico 16S/genética , Rhodospirillaceae/genética , Rhodospirillaceae/crecimiento & desarrollo , Agua de Mar/microbiología , Resultado del TratamientoRESUMEN
BACKGROUND: Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive. RESULTS: We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages. CONCLUSION: Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages.
Asunto(s)
Evolución Biológica , Genoma Bacteriano , Magnetosomas/genética , Rhodospirillaceae/genética , Proteínas Bacterianas/genética , Genómica , Luz , Magnetosomas/efectos de la radiación , Filogenia , Rhodospirillaceae/efectos de la radiaciónRESUMEN
Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant'Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29-4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca R. santandreae's versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts-serving as the primary energy storage for its animal host.
Asunto(s)
Genoma Bacteriano/genética , Platelmintos , Rhodospirillaceae , Simbiosis , Animales , Crecimiento Quimioautotrófico/genética , Crecimiento Quimioautotrófico/fisiología , Redes y Vías Metabólicas , Platelmintos/metabolismo , Platelmintos/microbiología , Platelmintos/fisiología , Rhodospirillaceae/genética , Rhodospirillaceae/fisiología , Simbiosis/genética , Simbiosis/fisiologíaRESUMEN
MicroRNAs (miRNAs) are key players in regulation of gene expression at post-transcription level in eukaryotic cells. MiRNAs have been intensively studied in plants, animals and viruses. The investigations of bacterial miRNAs have gained less attention, except for the recent studies on miRNAs derived from Streptococcus mutans ATCC 25175 and Escherichia coli DH10B. In this study, high-throughput sequencing approach was employed to investigate the miRNA population in bacteria of the genus Thalassospira using both the miRDeep2 and CID-miRNA methods. A total of 984 putative miRNAs were identified in 9 species of the genus Thalassospira using both miRDeep and CID-miRNA analyses. Fifty seven conserved putative miRNAs were found in different species of the genus Thalassospira, and up to 6 miRNAs were found to be present at different locations in the T. alkalitolerans JCM 18968T, T. lucentensis QMT2T and T. xianhensis P-4T. None of the putative miRNAs was found to share sequence to the reported miRNAs in E. coli DH10B and S. mutans ATCC 25175. The findings provide a comprehensive list of computationally identified miRNAs in 9 bacterial species of the genus Thalassospira and addressed the existing knowledge gap on the presence of miRNAs in the Thalassospira genomes.
Asunto(s)
Organismos Acuáticos/genética , MicroARNs , Rhodospirillaceae/genética , Biología Computacional , Regulación Bacteriana de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Agua de Mar/microbiología , Análisis de Secuencia de ARNRESUMEN
Filamentous cluster III Defluviicoccus (DF3) are known to proliferate and cause bulking issues in industrial wastewater treatment plants. Members of the genus Defluviicoccus are also known to exhibit the glycogen accumulating organism (GAO) phenotype, which is suggested to be detrimental to enhanced biological phosphorus removal (EBPR). Despite the reported negative impact members of the DF3 have on activated sludge wastewater treatment systems, limited research has focused on understanding the physiological traits that allow them to compete in these environments. In this study, a near complete genome of an abundant filamentous DF3 named 'Candidatus Defluviicoccus seviourii' was obtained from a full-scale sequencing batch reactor (SBR) treating winery wastewater. Annotation of the 'Ca. D. seviourii' genome revealed interesting metabolic features that help to understand the abundance of this microorganism in industrial wastewater treatment plants. Their potential for the storage of polyhydroxyalkanoates (PHA) is suggested to favour these organisms with the intermittent availability of carbon in these systems. An ability to fix nitrogen and take up urea may provide them with an additional advantage with the characteristically high carbon to nitrogen content of industrial waste. The genome and preliminary findings of this study provide a foundation for further research into these biotechnologically relevant organisms.
Asunto(s)
Reactores Biológicos/microbiología , Residuos Industriales/análisis , Rhodospirillaceae/genética , Rhodospirillaceae/metabolismo , Eliminación de Residuos Líquidos , Aguas Residuales/microbiología , Carbono/metabolismo , Genoma Bacteriano/genética , Genómica , Glucógeno , Nitrógeno/metabolismo , Fósforo/metabolismo , Rhodospirillaceae/clasificación , Aguas del AlcantarilladoRESUMEN
A novel basophilic bacterial strain, designated as SCSIO 08040T, was recovered from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-negative, vibrioid or spiral, light pink, 0.6-1.0 µm wide and 1.0-2.5 µm long. Growth occurred at 20-45 °C, pH 7-11 and <5â% (w/v) NaCl, with optimum growth at 28-37 °C, pH 7 and 0-3â% (w/v) NaCl. Catalase-, oxidase and urease-positive, nitrate reduction-negative. Analysis of 16S rRNA gene sequencing revealed that strain SCSIO 08040T had the highest similarity of 95.3â% to Rhodocista pekingensis 3-pT. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences showed that the novel isolate formed a distinct phylogenetic lineage in the family Rhodospirillaceae. The whole-cell hydrolysate contained meso-diaminopimelic acid, galactose, mannose and xylose. The total cellular fatty acid profile was dominated by C18:1ω7c and C19:0cycloω8c. Q-10 was the predominant ubiquinone. The major phospholipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. The DNA G+C content of strain SCSIO 08040T was 66.82 mol%. Based on these polyphasic data, a new genus, Indioceanicola gen. nov., is proposed in the family Rhodospirillaceae with the type species Indioceanicola profundi sp. nov. and the type strain SCSIO 08040T (=DSM 105146T=CGMCC 1.15812T).
Asunto(s)
Sedimentos Geológicos/microbiología , Filogenia , Rhodospirillaceae/clasificación , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Océano Índico , Fosfolípidos/química , Pigmentación , ARN Ribosómico 16S/genética , Rhodospirillaceae/genética , Rhodospirillaceae/aislamiento & purificación , Análisis de Secuencia de ADN , Ubiquinona/análogos & derivados , Ubiquinona/químicaRESUMEN
A clinical case study involving a man (35-49 years of age) with wounds to his lower right extremity. An isolate was sent to the Delaware Public Health Laboratory for confirmatory testing by genetic analysis of the 16S gene. Testing identified the isolate as a novel genus and species, Haematospirillum jordaniae.
Asunto(s)
Infecciones por Bacterias Gramnegativas/diagnóstico , Infecciones por Bacterias Gramnegativas/microbiología , Rhodospirillaceae/clasificación , Adulto , Antibacterianos/uso terapéutico , Técnicas Bacteriológicas , Infecciones por Bacterias Gramnegativas/tratamiento farmacológico , Humanos , Masculino , Persona de Mediana Edad , ARN Ribosómico 16S/genética , Rhodospirillaceae/genética , Rhodospirillaceae/aislamiento & purificación , Resultado del Tratamiento , Infección de Heridas/diagnóstico , Infección de Heridas/tratamiento farmacológico , Infección de Heridas/microbiologíaRESUMEN
Two novel marine bacteria, designated strains CSC3H3T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10-40 °C, pH 5-10 and in the presence of 0-15â% (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira, and shared 97.5-98.3â% sequence similarity to all other validly type strains of the genus Thalassospira, and the highest similarity was to the type strain Thalassospira povalilyticaZumi 95T (98.3â%), followed by Thalassospira australica NP3b2T (98.2â%). The digital DNA-DNA hybridization value between the two strains was 80.4â%, while the values with T. povalilyticaZumi 95T and T. australica NP3b2T were only 20.5-20.7â% and 20.4-20.5â%, respectively. The two strains possess similar major cellular fatty acids including C18â:â1ω7c, C16â:â0, C19â:â0ω8c cyclo, C18â:â1 2-OH and C17â:â0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3T (=MCCC 1A11786T=KCTC 62333T).
Asunto(s)
Filogenia , Rhodospirillaceae/clasificación , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , China , ADN Bacteriano/genética , Ácidos Grasos/química , Hibridación de Ácido Nucleico , Fosfolípidos/química , ARN Ribosómico 16S/genética , Rhodospirillaceae/genética , Rhodospirillaceae/aislamiento & purificación , Análisis de Secuencia de ADN , Ubiquinona/químicaAsunto(s)
Fascitis Necrotizante/diagnóstico , Infecciones por Bacterias Gramnegativas/diagnóstico , Rhodospirillaceae/aislamiento & purificación , Anciano , Antibacterianos/uso terapéutico , Diagnóstico Diferencial , Fascitis Necrotizante/complicaciones , Infecciones por Bacterias Gramnegativas/complicaciones , Infecciones por Bacterias Gramnegativas/tratamiento farmacológico , Humanos , Masculino , Filogenia , ARN Ribosómico 16S/química , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismo , Rhodospirillaceae/clasificación , Rhodospirillaceae/genética , Sepsis/diagnóstico , Análisis de Secuencia de ADNRESUMEN
Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp.), and is currently used in a sugarcane consortium inoculant with four other nitrogen-fixing bacterial strains. The present paper describes a significant improvement in the genome sequence and assembly for the N. amazonense strain CBAmC, and determination for the first time of a complete genome sequence for this bacterial species, using PacBio technology. The analysis of the genomic data obtained allowed the discovery of genes coding for metabolic pathways and cellular structures that may be determinant for the success of the bacterial establishment and colonization into the host sugarcane plant, besides conferring important characteristics to the inoculant. These include genes for the use of sucrose and N-glycans, biosynthesis of autoinducer molecules, siderophore production and acquisition, auxin and polyamine biosynthesis, flagellum, σ-fimbriae, a variety of secretion systems, and a complete denitrification system. Concerning genes for nitrogenase and auxiliary proteins, it was possible to corroborate literature data that in N. amazonense these probably had originated from horizontal gene transfer, from bacteria of the Rhizobiales order. The complete genomic sequence of the CBAmC strain of N. amazonense revealed that the bacterium harbors four replicons, including three chromosomes and one chromid, a profile that coincides with that of other two strains, according to literature data, suggesting that as a replicon pattern for the species. Finally, results of phylogenomic analyses in this work support the recent reclassification of the species, separating it from the Azospirillum genus. More importantly, results of the present work shall guide subsequent studies on strain CBAmC as well as the development of a sugarcane inoculant.
Asunto(s)
Genoma Bacteriano , Fijación del Nitrógeno , Tallos de la Planta/microbiología , Rhodospirillaceae/genética , Saccharum/microbiología , Rhodospirillaceae/aislamiento & purificaciónRESUMEN
Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.
Asunto(s)
Poríferos/microbiología , Rhodospirillaceae/metabolismo , Simbiosis/fisiología , Animales , Carbono/metabolismo , Genoma Bacteriano/genética , Metagenoma , Metagenómica , Microbiota , Nitrógeno/metabolismo , Filogenia , Rhodospirillaceae/genética , Azufre/metabolismoRESUMEN
Two isolates of bacterial strains A15T and A17 were isolated from stream bank soil in Kyonggi University. Cells were aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, non-spore-forming, rod-shaped, opaque, and cream coloured. Both strains hydrolysed CM-cellulose. Strains were able to grow at 20-42 °C, pH 5.5-10.0 and at 1.5â% NaCl concentration (w/v). Indole test was positive. Analyses of phylogenetic trees based on its 16S rRNA gene sequences indicated that strain A15T formed a lineage within the family Rhodospirillaceae of the phylum Proteobacteria which was distinct from Ferrovibrio denitrificans S3T (98.4â% sequence similarity) and Ferrovibrio xuzhouensis LM-6T (97.4â%). The sole detected respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The major cellular fatty acids were C19â:â0 cycloω8c, C16â:â0, summed feature 8 (C18â:â1ω7c and/or C18â:â1ω6c), C18â:â0cyclo and C12â:â0. The DNA G+C contents of strains A15T and A17 were 63.4 and 62.9 mol%, respectively. DNA-DNA relatedness between strain A15T and other two members of the genus Ferrovibrioranged from 25 to 37â%. The polyphasic characterization revealed strains A15T and A17 represent a novel species in the genus Ferrovibrio, for which the name Ferrovibriosoli sp. nov. is proposed. The type strain is A15T (=KEMB 9005-522T=KACC 19102T=NBRC 112682T).
Asunto(s)
Filogenia , Rhodospirillaceae/clasificación , Ríos , Microbiología del Suelo , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Hibridación de Ácido Nucleico , Fosfolípidos/química , ARN Ribosómico 16S/genética , República de Corea , Rhodospirillaceae/genética , Rhodospirillaceae/aislamiento & purificación , Análisis de Secuencia de ADN , Ubiquinona/químicaRESUMEN
A bacterial strain, 1-14T, was isolated from cyanobacterial aggregates in a eutrophic lake, Taihu Lake, China. Cells were observed to be slightly curved, rod-shaped, aerobic and Gram-stain-negative. Optimal growth occurred at pH 7.0 (range: 5.0-9.0), 28 °C (range: 20-32 °C) and 0â% (w/v) NaCl (range: 0-1.0â%) in R2A broth. No growth is observed at 37 °C. The cells were found to be positive for oxidase and catalase activities. The major respiratory quinone was ubiquinone Q-10. The major fatty acids (>10â%) were identified as C18â:â1ω6c/C18â:â1ω7c, C16â:â0 3-OH and C18â:â1 2-OH. The major polar lipids were found to consist of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine. Within the genus Niveispirillum, strain 1-14T was most closely related to Niveispirillum cyanobacteriorum TH16T (98.3â% 16S rRNA gene sequence similarity), followed by Niveispirillum irakense DSM 11586T (97.8â%) and Niveispirillum fermenti CC-LY736T (97.0â%). The genomic G+C content of strain 1-14T was 62.2 mol% based on total genome calculations. Genes coding for light-harvesting complexes LHI and LHII, and a photosynthetic reaction centre were detected in the genome. Average nucleotide identities and digital DNA-DNA hybridizations for complete genomes ranged from 76.4 to 83.5 and from 21.5 to 27.4â% between strain 1-14T and strains within the genus Niveispirillum. The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggested that strain 1-14T represents a novel species within the genus Niveispirillum, for which the name Niveispirillum lacus sp. nov. is proposed. The type strain is 1-14T (=CGMCC 1.12980T=LMG 28363T).