Metagenome-Assembled Genome Sequence of
            <i>Phormidium</i>
            sp. Strain SL48-SHIP, Isolated from the Microbial Mat of Salt Lake Number 48 (Novosibirsk Region, Russia)

Розанов, А. С.; Shipova, Aleksandra A.; Bryanskaya, A. V.; Peltek, S. E.

doi:10.1128/mra.00651-19

Cited by 4 publications

(4 citation statements)

References 9 publications

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“…P-1104 ) and several metagenome-assembled genomes ( Phormidium sp. SL48-SHIP 9 ( Rozanov et al, 2019 ) Phormidium sp.OSCR ( Nelson William et al, 2016 ), and Phormidium alkaliphilum ( Ataeian et al, 2021 ) ) have draft genomes . To further resolve the phylogenetic context of P. yuhuli AB48, another maximum likelihood tree was constructed from a more stringently defined set of 50 concatenated, single-copy marker genes shared amongst P. yuhuli AB48 and the draft genomes in this genus.…”

Section: Resultsmentioning

confidence: 99%

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Koch

Noonan

Qiu

et al. 2022

Front. Bioeng. Biotechnol.

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Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

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Section: Resultsmentioning

confidence: 99%

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Koch

Noonan

Qiu

et al. 2022

Front. Bioeng. Biotechnol.

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“…OSCR Cole et al, 2014 GCA_001314905 Phormidium sp. SL48-SHIP Rozanov et al, 2019 GCA_004299065 Phormidium lacuna HE10JO Nies et al., (2017) GCF_900149785 Phormidium willei BDU 130791 N/A GCF_001637315 LCM Bin17 (C1) Zorz et al., (2019) GCA_007692715 Cyanobacterium B1Sed10_56 Vavourakis et al., (2018) GCA_003550805 Nodosilinea sp. P-1105 Samylina et al, 2014 GCF_012911975 Leptolyngbya sp.…”

Section: Methodsmentioning

confidence: 99%

Proteome and strain analysis of cyanobacterium Candidatus “Phormidium alkaliphilum” reveals traits for success in biotechnology

et al. 2021

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Summary Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications.

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“…Por otra parte, ha sido investigada la estrategia de supervivencia de Nostoc flagelliforme en condiciones extremas de desecación y radiación UV, su genoma secuenciado presentó 8 363 872 pb, ocho plásmidos que van de 28 479 a 805 120 pb, 6909 genes y un contenido promedio de GC de 41-43% (Shang et al, 2019). Por último, se encuentra el genoma secuenciado de Phormidium sp., otra cianobacteria f ilamentosa abundante en las biocostras, su genoma está compuesto por 4 384 607 pb, 3807 genes y su contenido promedio de GC es del 52% (Rozanov et al, 2019). El análisis genómico de estas cianobacterias sugiere la presencia de múltiples genes involucrados en procesos de fotosíntesis, tolerancia a la desecación, respuesta a la radiación UV a través de maquinaria enzimática implicada en procesos de reparación de ADN, así como de otras características que contribuyen a que estos microorganismos sean componentes importantes de la biocostra (Starkenburg et al, 2011;Shang et al, 2019;Churro et al, 2020).…”

Section: Genómicaunclassified

Tecnologías ómicas para la exploración de la biocostra del suelo

Godoy¹,

González-Escobedo

2022

Terra Latinoam

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Las tecnologías “ómicas” son herramientas novedosas que facilitan el estudio de las comunidades microbianas de distintos ecosistemas, particularmente de la costra biológica del suelo, también llamada biocostra. Entre estas tecnologías se encuentran la genómica, transcriptómica, proteómica, metabolómica y metagenómica, que son utilizadas para analizar la diversidad y las funciones que llevan a cabo los microorganismos a través del estudio de sus biomoléculas y vías metabólicas. Entre los microorganismos que habitan la biocostra destacan las cianobacterias, las cuales son un grupo de bacterias fototróficas encargadas de realizar procesos importantes en el suelo, tal como la fijación de nitrógeno atmosférico, carbono orgánico, síntesis de clorofila y ficobilinas, así como la producción de exopolisacáridos para mejorar la estabilidad y fertilidad del suelo. Por lo tanto, el objetivo de la presente revisión es el de explorar la diversidad y la función que desempeñan estas comunidades microbianas en la biocostra, particularmente las cianobacterias, destacando los estudios realizados mediante el uso de las tecnologías ómicas. El conocimiento generado en los últimos años a través de las tecnologías ómicas ha demostrado la limitada cobertura que presentan las técnicas moleculares tradicionales, resultando en una subestimación de la diversidad real de las comunidades microbianas. Además, se ha mejorado la comprensión de los procesos ecológicos desarrollados por los microorganismos en beneficio de la biocostra, así como las capacidades funcionales individuales y colectivas, las cuales servirán como línea base para proponer estrategias importantes que solucionen la problemática de la degradación de los suelos.

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Metagenome-Assembled Genome Sequence of Phormidium sp. Strain SL48-SHIP, Isolated from the Microbial Mat of Salt Lake Number 48 (Novosibirsk Region, Russia)

Abstract: The Phormidium sp. strain SL48-SHIP genome was obtained from metagenomics sequencing of the microbial mat of Salt Lake No. 48 (54.201806 N, 78.179194 E; Novosibirsk Region, Russia). The sequenced and annotated genome is 4,384,607 bp and encodes 3,807 genes.

Cited by 4 publications

References 9 publications

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Proteome and strain analysis of cyanobacterium Candidatus “Phormidium alkaliphilum” reveals traits for success in biotechnology

Tecnologías ómicas para la exploración de la biocostra del suelo

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