Based on the model gram-negative bacteria Escherichia coli, cyanobacteria are commonly assumed to be monoploid [50]. However, these organisms can become oligoploid during rapid growth [51, 52]. Cyanobacteria may also contain several chromosome copies throughout their life cycles [50, 53, 54]. Previous studies reported polyploidy in several genera, such as Anabaena (Nostoc) [55], Synechococcus [56], and Synechocystis [57]. Here, Nostoc sphaeroides CCNUC1, Crocosphaera subtropica ATCC 51142 [58] and Anabaena (Dolichospermum) sp. 90 [59] were found to possess extra chromosomes. In contrast, large plasmids, or previously named “chromids” (considered here as > 500 kb), occurred in several genomes and were found in 11 genomes from four of the six analyzed cyanobacterial orders.
Chromids are large, plasmid-like replicons that were previously found in approximately 10% of bacterial genomes [48]. Chromids possess replication systems that are similar to plasmids and can carry essential genes for cell viability [60]. One of the proposed functions of these large replicons is to increase genome plasticity through the rapid acquisition or loss of genes by HGT [61]. Here, chromids occurred in approximately 15% of the analyzed cyanobacterial genomes, and therefore seem to be more widespread in cyanobacteria than in other phyla [48].
Nostoc sp. strain ATCC 53789 is a known producer of the antiproliferative cytotoxin cryptophycin, which is encoded in a plasmid [62, 63]. Other plasmidial BGCs found here, such as the hepatotoxin microcystin, antifungal hassallidin, and odorous terpenoid geosmin, contained all the core genes and are possibly functional [64–66]. Consistent with our results, plasmids have been previously shown to contain genes encoding RiPPs and are associated with the products of these toxic and odorous compounds [29, 67]. Toxins produced by other bacteria, such as botulinum from Clostridium botulinum and cereulide from Bacillus cereus, are also found on plasmids [68, 69]. In the case of the botulinum toxin, HGT of the botulinum gene cluster by conjugative plasmids < 200 kb is likely [70].
Only the plasmid pCC7120α from Nostoc sp. PCC7120 has been reported to be transmissible [71]. Nevertheless, our results indicate that other cyanobacterial plasmids are possibly conjugative. A previous study using automatic annotation found no homologs of the T4SS in cyanobacteria and hypothesized that an unknown mechanism of conjugation could be present in these organisms [72]. It is currently unclear whether cyanobacterial plasmids are predominantly immobile, unlike in other bacterial phyla, due to the reduced availability of cyanobacterial genome sequences [72].
NRPSs and PKSs are constituted by multi-domains that have specific functions in the biosynthetic pathways of polyketides and non-ribosomal peptides [73, 74]. While the core module of an NRPS consists of at least the adenylation, condensation, and peptidyl carrier protein modules, acyltransferase, acyl carrier protein, and a ketoacyl synthase are the core domains of a PKS [75, 76]. Thus, carrier proteins, such as the PPTs, are essential for the biosynthesis of these natural products. Two main families of PPTs are known, namely AcpS-type PPTs, which are involved in activating carrier proteins involved in the primary metabolism, and Sfp-like PPTs, which are involved in secondary metabolism pathways [9, 77].
In cyanobacteria, only one copy of Sfp-like PPTs had previously been found in 29 different genomes [78]. However, the present study revealed that some cyanobacterial genomes can encode up to three different PPTs. Other bacteria also contain multiple copies of these enzymes in their genomes [10, 79]. Interestingly, the fact that a plasmid from Acaryochloris marina MBIC11017 was the only representative of an AcpS-like PPT indicates that this enzyme could possibly be transferred horizontally together with BGCs. Consistent with our results, plasmids from other bacterial phyla have also been found to encode PPTs [80, 81].
RiPPs gene clusters were located in almost all analyzed genomes. These molecules are products of post-translational modification of ribosomally synthesized precursor peptides [82]. Thus far, over 20 families of compounds that possess unique chemical features have been proposed [82]. Cyanobacteria encode the machinery to produce several RiPPs, including cyanobactins [83], lanthipeptides [84], lassopeptides [85], and microviridins [86]. Although cyanobactin BGCs are widespread in cyanobacteria and initially received the most attention, other RiPPs from cyanobacteria are also being explored [29, 84]. Considering that automated tools are being improved to better predict genes involved in the biosynthesis of these compounds, future studies may expand the known repertoire of RiPPs produced by cyanobacteria [47, 87].
Although terpenes are commonly isolated from plants and fungi, genes involved in their biosynthesis are widely found in bacterial genomes [88]. These compounds are essential in primary metabolism, such as for photosynthesis and respiration, but also have roles as secondary metabolites [89]. This could explain why genes encoding enzymes involved in the biosynthesis of terpenes are present in cyanobacterial genomes [90]. In cyanobacteria, geosmin and 2-methylisoborneol are widely studied terpenes as they are odorous metabolites that impact drinking water quality [64, 91, 92]. Nevertheless, the repertoire of terpenes produced by cyanobacteria is possibly larger than currently known, as various cryptic terpene synthases are found in their genomes [30, 88].