scholarly journals Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica

2013 ◽  
Vol 79 (8) ◽  
pp. 2542-2551 ◽  
Author(s):  
Takashi Okubo ◽  
Shohei Fukushima ◽  
Manabu Itakura ◽  
Kenshiro Oshima ◽  
Aphakorn Longtonglang ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Gene Clusters ◽  
Nodule Development ◽  
Nitrogen Fixing ◽  
Circular Chromosome ◽  
Nod Factor ◽  
Content Type ◽  
Oligotrophic Bacterium

ABSTRACTAgromonas oligotrophica(Bradyrhizobium oligotrophicum) S58Tis a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lackingnodABCgenes and the typical symbiosis island. The genome showed a high level of similarity to the genomes ofBradyrhizobiumsp. ORS278 andBradyrhizobiumsp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant,Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nifandfix) withA. indicawere well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with fiveA. oligotrophicastrains (S58, S42, S55, S72, and S80). Surprisingly, all five strains ofA. oligotrophicaformed effective nitrogen-fixing nodules on the roots and/or stems ofA. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwellingA. oligotrophicagenerally possesses the ability to establish symbiosis withA. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis withA. indicais a common trait ofnodABC- and symbiosis island-lacking strains within the members of the photosyntheticBradyrhizobiumclade, includingA. oligotrophica.

scholarly journals Sinorhizobium melilotiGlutathione Reductase Is Required for both Redox Homeostasis and Symbiosis

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Guirong Tang ◽  
Ningning Li ◽  
Yumin Liu ◽  
Liangliang Yu ◽  
Junhui Yan ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Sinorhizobium Meliloti ◽  
De Novo ◽  
Redox Homeostasis ◽  
Nodule Development ◽  
Glutathione Synthetase ◽  
Insertion Mutation ◽  
Nitrogen Fixing ◽  
Content Type ◽  
In Cells

ABSTRACTGlutathione (l-γ-glutamyl-l-cysteinylglycine) (GSH), one of the key antioxidants inSinorhizobium meliloti, is required for the development of alfalfa (Medicago sativa) nitrogen-fixing nodules. Glutathione exists as either reduced glutathione (GSH) or oxidized glutathione (GSSG), and its content is regulated by two pathways inS. meliloti. The first pathway is thede novosynthesis of glutathione from its constituent amino acids, namely, Glu, Cys, and Gly, catalyzed by γ-glutamylcysteine synthetase (GshA) and glutathione synthetase (GshB). The second pathway is the recycling of GSSG via glutathione reductase (GR). However, whether theS. melilotiGR functions similarly to GshA and GshB1 during symbiotic interactions with alfalfa remains unknown. In this study, a plasmid insertion mutation of theS. melilotigorgene, which encodes GR, was constructed, and the mutant exhibited delayed alfalfa nodulation, with 75% reduction in nitrogen-fixing capacity. Thegormutant demonstrated increased accumulation of GSSG and a decreased GSH/GSSG ratio in cells. The mutant also showed defective growth in rich broth and minimal broth and was more sensitive to the oxidants H2O2and sodium nitroprusside. Interestingly, the expression ofgshA,gshB1,katA, andkatBwas induced in the mutant. These findings reveal that the recycling of glutathione is important forS. melilotito maintain redox homeostasis and to interact symbiotically with alfalfa.IMPORTANCEThe antioxidant glutathione is regulated by its synthetase and reductase in cells. In the symbiotic bacteriumS. meliloti, thede novosynthesis of glutathione is essential for alfalfa nodulation and nitrogen fixation. In this study, we observed that the recycling of glutathione from GSSG not only was required for redox homeostasis and oxidative stress protection inS. meliloticells but also contributed to alfalfa nodule development and competition capacity. Our findings demonstrate that the recycling of glutathione plays a key role in nitrogen fixation symbiosis.

scholarly journals Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

2020 ◽  
Vol 70 (9) ◽  
pp. 5063-5074 ◽  
Author(s):  
Sawa Wasai-Hara ◽  
Kiwamu Minamisawa ◽  
Sylvie Cloutier ◽  
Eden S. P. Bromfield
Keyword(s):  
Nitrogen Fixation ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Taxonomic Status ◽  
Gene Clusters ◽  
Genomic Islands ◽  
Content Type ◽  
Link Type ◽  
Contrasting Habitats ◽  
Photosynthesis Gene

The taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.

scholarly journals Complete Genome Sequence of Streptococcus pneumoniae Strain Rx1, a Hex Mismatch Repair-Deficient Standard Transformation Recipient

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
Anna Maria Cuppone ◽  
Lorenzo Colombini ◽  
Valeria Fox ◽  
David Pinzauti ◽  
Francesco Santoro ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Mismatch Repair ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Content Type ◽  
Sequencing Technologies

The complete genome sequence of Streptococcus pneumoniae strain Rx1, a Hex mismatch repair-deficient standard transformation recipient, was obtained by combining Nanopore and Illumina sequencing technologies. The genome consists of a 2.03-Mb circular chromosome, with 2,054 open reading frames and a GC content of 39.72%.

scholarly journals Draft Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas pseudoalcaligenes KB-10

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
M. M. A. Khan ◽  
Jin Duan ◽  
Bernard R. Glick ◽  
Patrick M. Finnegan ◽  
Saleh A. Kabli ◽  
...  
Keyword(s):  
Plant Growth ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Circular Chromosome ◽  
Pseudomonas Pseudoalcaligenes ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Pseudomonas pseudoalcaligenes KB-10 can enhance salinity tolerance in coriander plants. We report a draft genome sequence of P. pseudoalcaligenes KB-10, comprising a 5,241,174-bp circular chromosome containing 4,921 genes, with a GC content of 62.97%.

scholarly journals Draft Genome Sequence of Streptomyces cavourensis YBQ59, an Endophytic Producer of Antibiotics Bafilomycin D, Nonactic Acid, Prelactone B, and 5,11-Epoxy-10-Cadinanol

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Huy Quang Nguyen ◽  
Nguyen Thi-Hanh Vu ◽  
Ha Hoang Chu ◽  
Son Ky Chu ◽  
Ha Hoang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Biosynthetic Pathways ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

This study reports the draft genome sequence of the endophytic Streptomyces cavourensis strain YBQ59, produces the antibiotics bafilomycin D, nonactic acid, prelactone B, and 5,11-epoxy-10-cadinanol. The draft genome sequence comprises ∼10.2 Mb, with a GC content of 64% and 8,958 predicted protein-coding genes, of which 14 gene clusters were found to associate with antibiotic biosynthetic pathways.

scholarly journals Draft Genome Sequence of Lactobacillus rhamnosus OSU-PECh-69, a Cheese Isolate with Antibacterial Activity

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Israel García-Cano ◽  
Walaa E. Hussein ◽  
Diana Rocha-Mendoza ◽  
Ahmed E. Yousef ◽  
Rafael Jiménez-Flores
Keyword(s):  
Genome Sequence ◽  
Antimicrobial Agents ◽  
Draft Genome ◽  
Lactobacillus Rhamnosus ◽  
Gc Content ◽  
Gene Clusters ◽  
Gram Negative Bacteria ◽  
The Novel ◽  
Content Type ◽  
A Genome

ABSTRACT The novel strain Lactobacillus rhamnosus OSU-PECh-69 was isolated from provolone cheese. It produces antimicrobial agents having a molecular mass of 5 to 10 kDa that are active against Gram-positive and Gram-negative bacteria. The strain has a genome sequence of 3,057,669 bp, a GC content of 46.6%, and up to two gene clusters encoding bacteriocins.

scholarly journals Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Sohaib Sarfraz ◽  
Saïd Oulghazi ◽  
Jérémy Cigna ◽  
Shahbaz Talib Sahi ◽  
Kashif Riaz ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Gc Content ◽  
Illumina Miseq ◽  
Blackleg Disease ◽  
Circular Chromosome ◽  
Content Type ◽  
Potato Plants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

scholarly journals Nutrient-ColimitedTrichodesmiumas a Nitrogen Source or Sink in a Future Ocean

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Nathan G. Walworth ◽  
Fei-Xue Fu ◽  
Michael D. Lee ◽  
Xiaoni Cai ◽  
Mak A. Saito ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Organic Nitrogen ◽  
Open Ocean ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Nitrogen Inputs ◽  
Ocean Conditions ◽  
Nitrogen Scavenging

ABSTRACTNitrogen-fixing (N2) cyanobacteria provide bioavailable nitrogen to vast ocean regions but are in turn limited by iron (Fe) and/or phosphorus (P), which may force them to employ alternative nitrogen acquisition strategies. The adaptive responses of nitrogen fixers to global-change drivers under nutrient-limited conditions could profoundly alter the current ocean nitrogen and carbon cycles. Here, we show that the globally important N2fixerTrichodesmiumfundamentally shifts nitrogen metabolism toward organic-nitrogen scavenging following long-term high-CO2adaptation under iron and/or phosphorus (co)limitation. Global shifts in transcripts and proteins under high-CO2/Fe-limited and/or P-limited conditions include decreases in the N2-fixing nitrogenase enzyme, coupled with major increases in enzymes that oxidize trimethylamine (TMA). TMA is an abundant, biogeochemically important organic nitrogen compound that supports rapidTrichodesmiumgrowth while inhibiting N2fixation. In a future high-CO2ocean, this whole-cell energetic reallocation toward organic nitrogen scavenging and away from N2fixation may reduce new-nitrogen inputs byTrichodesmiumwhile simultaneously depleting the scarce fixed-nitrogen supplies of nitrogen-limited open-ocean ecosystems.IMPORTANCETrichodesmiumis among the most biogeochemically significant microorganisms in the ocean, since it supplies up to 50% of the new nitrogen supporting open-ocean food webs. We usedTrichodesmiumcultures adapted to high-CO2conditions for 7 years, followed by additional exposure to iron and/or phosphorus (co)limitation. We show that “future ocean” conditions of high CO2and concurrent nutrient limitation(s) fundamentally shift nitrogen metabolism away from nitrogen fixation and instead toward upregulation of organic nitrogen-scavenging pathways. We show that the responses ofTrichodesmiumto projected future ocean conditions include decreases in the nitrogen-fixing nitrogenase enzymes coupled with major increases in enzymes that oxidize the abundant organic nitrogen source trimethylamine (TMA). Such a shift toward organic nitrogen uptake and away from nitrogen fixation may substantially reduce new-nitrogen inputs byTrichodesmiumto the rest of the microbial community in the future high-CO2ocean, with potential global implications for ocean carbon and nitrogen cycling.

scholarly journals Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Jun Kong ◽  
Hongshan Jiang ◽  
Baiyun Li ◽  
Wenjun Zhao ◽  
Zhihong Li ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Strain Atcc ◽  
Circular Chromosome ◽  
Coding Sequences

Pseudomonas syringae pv. lapsa is a pathovar of Pseudomonas syringae that can infect wheat. The complete genome of P. syringae pv. lapsa strain ATCC 10859 contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16 rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome revealed several gene clusters that are related to pathogenesis and virulence.

scholarly journals Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Michael D. Lee ◽  
Eric A. Webb ◽  
Nathan G. Walworth ◽  
Fei-Xue Fu ◽  
Noelle A. Held ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Carbon Fixation ◽  
Community Respiration ◽  
Ecological Niches ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Globally Distributed

ABSTRACTTrichodesmiumis a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs,Trichodesmiumserves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated withTrichodesmium erythraeum(strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO2concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO2, potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community withinTrichodesmiumconsortia.IMPORTANCETrichodesmiumis a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of theTrichodesmiumgenus tend to form large macroscopic colonies that appear to perpetually host an association of diverse interacting microbes distinct from the surrounding seawater, potentially making the entire assemblage a unique miniature ecosystem. Since its first successful cultivation in the early 1990s, there have been questions about the potential interdependencies betweenTrichodesmiumand its associated microbial community and whether the host's seemingly enigmatic nitrogen fixation schema somehow involved or benefited from its epibionts. Here, we revisit these old questions with new technology and investigate gene expression activities of microbial communities living in association withTrichodesmium.

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