A Metagenomic Approach to Cyanobacterial Genomics

Abstract

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.

Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community

“…The presence of a microbial community in the HT-58-2 culture presented challenges in obtaining cyanobacterial DNA suitable for genomic sequencing. In this regard, filamentous cyanobacterial genomes are notorious for being difficult to assemble (32). Ultimately, a short growth period in the presence of 10% dimethyl sulfoxide (DMSO), followed by extensive washing of filaments with 10 to 20% DMSO and lysis of the resulting filaments under liquid nitrogen (cell preparation method 2 in Materials and Methods), yielded cyanobacterial genomic DNA that could Tolyporphin-Producing Cyanobacterium-Microbe Community Applied and Environmental Microbiology be assembled from PacBio SMRT cell sequencing reads (finishing and closing details are summarized in Table S3).…”

Morphological and Molecular Identification of Microcystin-Producing Cyanobacteria in Nine Shallow Bulgarian Water Bodies

“…The fact that only 12 (21%) of the sequences were affiliated to the strains of distinct species (M. aeruginosa and M. wesenbergii) provided a great challenge to assign all obtained toxigenic genotypes to certain Microcystis taxa. On the one hand, the low number of affiliations was due to the recent general low availability of genomic sequences from cyanobacteria when compared to other prokaryotes [47]. In the same time, five of the NCBI sequences used in the obtained phylogenetic tree (Figure 9) were based on metagenomic data (genetic material recovered directly from uncultured organisms from environmental samples- [48]).…”

“…In the same time, five of the NCBI sequences used in the obtained phylogenetic tree (Figure 9) were based on metagenomic data (genetic material recovered directly from uncultured organisms from environmental samples- [48]). Despite the increased application of these data in modern studies based on the common difficulties, or even impossibility, to culture some cyanobacteria [47], their use in identification work is problematic because of the lack of morphological descriptions for most of the sequenced uncultured strains. The same is the case of most axenic strains with fixed sequences, registered in the NCBI and used for obtaining the phylogenetic tree.…”

Comparative phylogeography of two free‐living cosmopolitan cyanobacteria: Insights on biogeographic and latitudinal distribution

“…The traditional classification and studies of cyanobacteria together with algae and plants, as well as the scarcity of qualified professionals to identify and classify taxa, have contributed to underestimation of their diversity and a lack of genetic information (Ribeiro et al, ). For instance, the number of cyanobacterial genomes amounts to approximately 0.6% of all available prokaryotic genomes (Alvarenga, Fiore, & Varani, ). This situation has contributed to a relative lack of attention to other aspects such as the biogeography and phylogeography of cyanobacteria.…”