scholarly journals Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

2006 ◽  
Vol 72 (3) ◽  
pp. 2050-2063 ◽  
Author(s):  
Shawn R. Starkenburg ◽  
Patrick S. G. Chain ◽  
Luis A. Sayavedra-Soto ◽  
Loren Hauser ◽  
Miriam L. Land ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Rhodopseudomonas Palustris ◽  
Type I ◽  
Nitrite Oxidation ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Gene Copies ◽  
Nitrite Oxidizing Bacteria ◽  
Genes Encoding ◽  
Nitrite Oxidoreductase

ABSTRACT The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.

scholarly journals Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707

2006 ◽  
Vol 72 (9) ◽  
pp. 6299-6315 ◽  
Author(s):  
Martin G. Klotz ◽  
Daniel J. Arp ◽  
Patrick S. G. Chain ◽  
Amal F. El-Sheikh ◽  
Loren J. Hauser ◽  
...  
Keyword(s):  
Tricarboxylic Acid Cycle ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Type I ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Terminal Electron Acceptor ◽  
Genes Encoding ◽  
Pentose Phosphate Pathways ◽  
Ammonia Oxidizing Bacterium

ABSTRACT The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).

scholarly journals Complete Genome Sequence of Actinomyces hongkongensis HKU8T Isolated from Human Blood

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Yan-xia Gao ◽  
Yu-yan Zhou ◽  
Ying Xie ◽  
Man Wang ◽  
Shu-juan Wang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Human Blood ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Human Diseases ◽  
Circular Chromosome ◽  
Content Type ◽  
Genes Encoding

ABSTRACT Members of the genus Actinomyces are strongly associated with human diseases. We present here the complete genome sequence of Actinomyces hongkongensis HKU8T, which consists of one circular chromosome. The strain characteristically contains various genes encoding for enzymes involved in arylamidase utilization.

scholarly journals Complete Genome Sequence of Pseudomonas syringae BIM B-268, a Plant Pathogen Strain Used for In Vitro Testing of Agricultural Bacteriophage Efficiency

2021 ◽  
Vol 10 (26) ◽  
Author(s):  
Rustam M. Buzikov ◽  
Tatsiana A. Pilipchuk ◽  
Leonid N. Valentovich ◽  
Emilia I. Kalamiyets ◽  
Andrey M. Shadrin
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Ice Nucleation ◽  
Secretion Systems ◽  
Ice Nucleation Protein ◽  
Circular Chromosome ◽  
Content Type ◽  
Genes Encoding ◽  
Single Circular Chromosome

Pseudomonas syringae BIM B-268 is the strain used for in vitro testing of the efficiency of Multiphage, a bacteriophage-based biopesticide produced in Belarus. The genome sequence of this strain consists of a single circular chromosome harboring the genes encoding the ice nucleation protein, syringopeptin biosynthesis, and types III and VI secretion systems.

scholarly journals Complete Genome Sequence of the Novel Psychrobacter sp. Strain AJ006, Which Has the Potential for Biomineralization

2020 ◽  
Vol 9 (41) ◽  
Author(s):  
Jun Ho Lee ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Novel ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Biomineralization Process ◽  
Chromosomal Genes ◽  
Genes Encoding ◽  
Single Circular Chromosome

ABSTRACT A novel Psychrobacter sp. strain, AJ006, was isolated from Antarctic soil. Its complete genome sequence consists of a single circular chromosome (3,032,533 bp; G+C content, 44.0%) and a single linear plasmid (49,070 bp; G+C content, 41.7%). Chromosomal genes encoding carbonic anhydrase and urease, key enzymes in a biomineralization process, were predicted.

scholarly journals Complete Genome Sequence of Yellow Pigment-Producing Sphingobium sp. Strain HAL-16

2020 ◽  
Vol 9 (41) ◽  
Author(s):  
Soon Jae Kwon ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Soil Samples ◽  
Yellow Pigment ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Genes Encoding ◽  
Single Circular Chromosome ◽  
Β Carotene

ABSTRACT Sphingobium sp. strain HAL-16, which was isolated from Antarctic soil samples, synthesizes a yellow pigment. The complete genome consists of a single circular chromosome (4,372,398 bp, with a G+C content of 62.7%) and a single circular plasmid (57,025 bp, with a G+C content of 59.4%). Five genes encoding carotenogenic enzymes were identified, suggesting that the yellow pigment is a hydroxy/keto-β-carotene.

scholarly journals Characterization of the First “CandidatusNitrotoga” Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Katharina Kitzinger ◽  
Hanna Koch ◽  
Sebastian Lücker ◽  
Christopher J. Sedlacek ◽  
Craig Herbold ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Nitrogen Cycle ◽  
Alternative Energy ◽  
Carbon Fixation ◽  
Metagenomic Data ◽  
Nitrite Oxidation ◽  
Metabolic Versatility ◽  
Nitrite Oxidizing Bacteria ◽  
Genes Encoding

ABSTRACTNitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus “CandidatusNitrotoga” are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure “Ca. Nitrotoga” culture was available. Here we obtained the first “Ca. Nitrotoga” isolate from activated sludge. This organism, “CandidatusNitrotoga fabula,” prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous “Ca. Nitrotoga” enrichments, which were described as cold-adapted NOB. “Ca. Nitrotoga fabula” also showed an unusually high tolerance to nitrite (activity at 30 mM NO2−) and nitrate (up to 25 mM NO3−). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparentKm(Km(app)) of ~89 µM nitrite and aVmaxof ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of “Ca. Nitrotoga fabula” were reconstructed from the closed genome. “Ca. Nitrotoga fabula” possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in “Ca. Nitrotoga” and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, “Ca. Nitrotoga fabula” uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable “Ca. Nitrotoga fabula” to survive nitrite depletion and colonize new niches.IMPORTANCENitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus “CandidatusNitrotoga” and performed a detailed physiological and genomic characterization of this organism (“CandidatusNitrotoga fabula”). Differences between key phenotypic properties of “Ca. Nitrotoga fabula” and those of previously enriched “Ca. Nitrotoga” members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that “Ca. Nitrotoga” are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in “Ca. Nitrotoga fabula” expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.

scholarly journals The Genome of Heliobacterium modesticaldum, a Phototrophic Representative of the Firmicutes Containing the Simplest Photosynthetic Apparatus

2008 ◽  
Vol 190 (13) ◽  
pp. 4687-4696 ◽  
Author(s):  
W. Matthew Sattley ◽  
Michael T. Madigan ◽  
Wesley D. Swingley ◽  
Patricia C. Cheung ◽  
Kate M. Clocksin ◽  
...  
Keyword(s):  
Purple Bacteria ◽  
Calvin Cycle ◽  
Photosynthetic Apparatus ◽  
Complete Sequence ◽  
Ribulose Bisphosphate Carboxylase ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Anoxygenic Phototrophs ◽  
Genes Encoding ◽  
Heliobacterium Modesticaldum

ABSTRACT Despite the fact that heliobacteria are the only phototrophic representatives of the bacterial phylum Firmicutes, genomic analyses of these organisms have yet to be reported. Here we describe the complete sequence and analysis of the genome of Heliobacterium modesticaldum, a thermophilic species belonging to this unique group of phototrophs. The genome is a single 3.1-Mb circular chromosome containing 3,138 open reading frames. As suspected from physiological studies of heliobacteria that have failed to show photoautotrophic growth, genes encoding enzymes for known autotrophic pathways in other phototrophic organisms, including ribulose bisphosphate carboxylase (Calvin cycle), citrate lyase (reverse citric acid cycle), and malyl coenzyme A lyase (3-hydroxypropionate pathway), are not present in the H. modesticaldum genome. Thus, heliobacteria appear to be the only known anaerobic anoxygenic phototrophs that are not capable of autotrophy. Although for some cellular activities, such as nitrogen fixation, there is a full complement of genes in H. modesticaldum, other processes, including carbon metabolism and endosporulation, are more genetically streamlined than they are in most other low-G+C gram-positive bacteria. Moreover, several genes encoding photosynthetic functions in phototrophic purple bacteria are not present in the heliobacteria. In contrast to the nutritional flexibility of many anoxygenic phototrophs, the complete genome sequence of H. modesticaldum reveals an organism with a notable degree of metabolic specialization and genomic reduction.

scholarly journals Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons

2019 ◽  
Vol 11 (10) ◽  
pp. 2818-2823 ◽  
Author(s):  
Fabíola de Jesus Silva ◽  
Larissa Carvalho Ferreira ◽  
Vicente Paulo Campos ◽  
Valter Cruz-Magalhães ◽  
Aline Ferreira Barros ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Hybridization ◽  
Related Species ◽  
Nucleotide Identity ◽  
Full Genome Sequence ◽  
Average Nucleotide Identity ◽  
Bacillus Velezensis ◽  
Circular Chromosome ◽  
Closely Related Species ◽  
Genes Encoding

Abstract In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.

scholarly journals Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones

2021 ◽  
Author(s):  
Xin Sun ◽  
Claudia Frey ◽  
Emilio Garcia-Robledo ◽  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Nitrogen Loss ◽  
Niche Differentiation ◽  
Nitrite Reduction ◽  
Nitrite Oxidation ◽  
Fixed Nitrogen ◽  
Anoxic Waters ◽  
Biogeochemical Models ◽  
Nitrite Oxidizing Bacteria ◽  
Oxygen Addition ◽  
Oxygen Minimum

AbstractNitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

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