Exploring cyanobacterial genomes for natural product biosynthesis pathways

Micallef, Melinda L.; D’Agostino, Paul M.; Al‐Sinawi, Bakir; Neilan, Brett A.; Moffitt, Michelle C.

doi:10.1016/j.margen.2014.11.009

Cited by 45 publications

(39 citation statements)

References 119 publications

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“…Another important physiological feature previously investigated in Parasynechococcus strains was their ability to produce bacteriocins (Wang et al 2011). Gene clusters encoding these secondary metabolites that have antimicrobial activities have been shown to be diverse and widespread in Cyanobacteria (Micallef et al 2015). These gene clusters are present in the proposed species in different combinations (Table 1).…”

Section: Diagnostic Physiological Featuresmentioning

confidence: 99%

“…Parasynechococcus is a dominant member of marine microbial communities and is among the most important contributors of global primary productivity (Flombaum et al 2013;Coutinho et al 2015). These organisms have developed diverse strategies for nutrient uptake (Palenik et al 2003), production of secondary metabolites (Micallef et al 2015) and light harvesting and utilization (Six et al 2007a, b). Nevertheless, no species have been described within this genus; thus, the taxonomic framework of this taxon remains uncharacterized.…”

Section: Introductionmentioning

confidence: 99%

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Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

et al. 2016

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Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.

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Section: Diagnostic Physiological Featuresmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

et al. 2016

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“…90 and Fischerella sp. PCC 9339 (Fiore et al, 2013;Frangeul et al, 2008;Humbert et al, 2013;Kaneko et al, 1996;Micallef, D'Agostino, Al-Sinawi, Neilan, & Moffitt, 2014;Rounge, Rohrlack, Nederbragt, Kristensen, & Jakobsen, 2009;Shih et al, 2013;Tooming-Klunderud et al, 2013;Wang et al, 2012). As , not to scale.…”

Section: Microcystinmentioning

confidence: 99%

Marine Microbial Secondary Metabolites

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Russo

et al. 2015

Advances in Microbial Physiology

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“…Some of these organisms cause ecological disturbances after blooming in natural and eutrophic waters, an event that is becoming more frequent as the climate changes (Paerl and Otten, 2013; Costa et al, 2016; Visser et al, 2016). In addition, cyanobacteria are a subject of scientific investigation in regard to their production of toxic and non-toxic secondary metabolites (Merel et al, 2013; Micallef et al, 2015; Pearson et al, 2016). Their troubled taxonomic history has also left an ongoing need for revisiting the systematics of this phylum (Hoffmann et al, 2005; Komárek et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

A Metagenomic Approach to Cyanobacterial Genomics

2017

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Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria.

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Exploring cyanobacterial genomes for natural product biosynthesis pathways

Cited by 45 publications

References 119 publications

Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

Marine Microbial Secondary Metabolites

A Metagenomic Approach to Cyanobacterial Genomics

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