Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

Background

Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood.

Results

We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways for the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways.

Conclusions

Therefore, in addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-977) contains supplementary material, which is available to authorized users.     

Anabaenolysins, novel cytolytic lipopeptides from benthic Anabaena cyanobacteria

Two novel cyclic lipopeptides, anabaenolysin A and anabaenolysin B, were isolated from two benthic cyanobacterial strains of the genus Anabaena. This novel class of cyanobacterial lipopeptides has a general structure of a small peptide ring consisting of four amino acids from which two are proteinogenic and two unusual; glycine(1), glycine(2), 2-(3-amino-5-oxytetrahydrofuran-2-yl)-2-hydroxyacetic acid(3) and a long unsaturated C(18) β-amino acid(4) with a conjugated triene structure. They are distinguished by the presence of a conjugated dienic structure in the C18 β-amino acid present in anabaenolysin A but not in anabaenolysin B. Conjugated triene structure generates a typical UV spectrum for anabaenolysins for easy recognition. Anabaenolysin A constituted up to 400 ppm of the cyanobacterial dry weight. We found evidence of thirteen variants of anabaenolysins in one cyanobacterial strain. This suggests that the anabaenolysins are an important class of secondary metabolites in benthic Anabaena cyanobacteria. Both anabaenolysin A and B had cytolytic activity on a number of mammalian cell lines.     

Optimal radio-tracking strategy — The best results with the least effort?

We tested the need to radio-track nocturnal mammals, such as raccoon dogsNyctereutes procyonoides (Gray, 1834) and badgersMeles meles (Linnaeus, 1758), throughout the night for reliable estimates of home range size and habitat selection. We also tested the possibility to reduce the tracking effort by decreasing the number of tracking-nights. The results indicated that the locations collected before midnight gave good estimates of home range sizes but those collected after midnight or by reducing the number of tracking-nights resulted in smaller home ranges than those estimated using the total data. Thus, if one aims to estimate only the home range size, locations before midnight would be adequate. Locations of raccoon dogs taken only before or after midnight did not reveal all habitats, which were favoured on the basis of the total data. Although locations of badgers before midnight seemed to give correct results of habitat selection, we recommend radio-tracking also badgers at least few times through the night, because their core areas shifted during the night. In the case of badgers, but not of raccoon dogs, we obtained correct results of habitat selection by reducing the tracking effort by decreasing the number of tracking-nights.     

Detection of microcystin-producing cyanobacteria in Finnish lakes with genus-specific microcystin synthetase gene E (mcyE) PCR and associations with environmental factors

We studied the frequency and composition of potential microcystin (MC) producers in 70 Finnish lakes with general and genus-specific microcystin synthetase gene E (mcyE) PCR. Potential MC-producing Microcystis, Planktothrixand Anabaena spp. existed in 70%, 63%, and 37% of the lake samples, respectively. Approximately two-thirds of the lake samples contained one or two potential MC producers, while all three genera existed in 24% of the samples. In oligotrophic lakes, the occurrence of only one MC producer was most common. The combination of Microcystis and Planktothrix was slightly more prevalent than others in mesotrophic lakes, and the cooccurrence of all three MC producers was most widespread in both eutrophic and hypertrophic lakes. The proportion of the three-producer lakes increased with the trophic status of the lakes. In correlation analysis, the presence of multiple MC-producing genera was associated with higher cyanobacterial and phytoplankton biomass, pH, chlorophyll a, total nitrogen, and MC concentrations. Total nitrogen, pH, and the surface area of the lake predicted the occurrence probability of mcyE genes, whereas total phosphorus alone accounted for MC concentrations in the samples by logistic and linear regression analyses. In conclusion, the results suggested that eutrophication increased the cooccurrence of potentially MC-producing cyanobacterial genera, raising the risk of toxic-bloom formation.     

Allelopathy of Baltic Sea cyanobacteria: no evidence for the role of nodularin

Extracts of Aphanizomenon flos-aquae and Nodularia spumigena,the two most common cyanobacteria forming recurrent blooms inthe Baltic Sea, decrease the abundance of some phytoplanktonspecies via the release of allelopathic substances. We investigatedhow cell-free filtrates of the two cyanobacteria, as well aspurified hepatotoxin nodularin, produced by N. spumigena affectedcell numbers, chlorophyll a content and ¹⁴CO₂ uptake of thecryptophyte Rhodomonas sp. Both cyanobacterial filtrates significantlyretarded the growth of Rhodomonas sp., A. flos-aquae filtrateup to 46%, whereas purified nodularin showed no significanteffect on any of the growth parameters of the cryptophyte. Theseresults suggest that the allelopathic effect of N. spumigenais most probably due to metabolite(s) other than nodularin,possibly acting via the damage of the target cells.     

The effect of prey quality and ice conditions on the nutritional status of Baltic gray seals of different age groups

We analyzed a long-term data set of the body condition of Baltic gray seals (Halichoerus grypus) over time and investigated how average subcutaneous blubber thickness of different age groups of seals corresponds to environmental factors. Blubber thickness of pups declined until 2010. The decreasing weight of 5–6-year-old herring (Clupea harengus), the main prey fish for Baltic gray seals, explained well the decline. In the Gulf of Finland, the blubber thickness of pups declined also in recent years (2011–2015) with declining number of days with permanent ice cover. In other regions, the blubber thickness of pups increased during recent years with increasing weight of herring. The blubber thickness of sub-adults in Baltic Proper and that of hunted adult females in the Bothnian Bay also increased during recent years, and the weight of age 6+ or 7-year-old herring best explained the increase. The blubber thickness of all age groups of seals was thinnest in the Bothnian Bay where also herring weight was lowest. There was a negative correlation between blubber thickness of seals and herring catch size (an index of herring abundance) suggesting that herring quality, not the quantity, is important for the nutritional status of Baltic gray seals. Nutritional status of gray seals may thus reveal changes in the marine food web which affect herring quality. Marine food web, in turn, may be affected, e.g., by climate change. The warming climate also has an impact on ice cover and thus body condition of seal pups.     

Physical and chemical characteristics of shallow embayments on the southern coast of Finland

Regular water-quality monitoring is yielding a great number of hydrographical and chemical data regarding the brackish Baltic Sea. However, present monitoring programmes often do not include shallow and sheltered near-shore areas, which are adjacent to human population and used for recreation purposes. We collected new near-shore water quality data from the southern coast of Finland that will allow the definition of the present state of these systems and may serve as reference data for possible future monitoring programmes. The data set comprises 45 small and shallow embayments with a mean surface area of 211 ha and a mean depth of 4.3 m. According to redundancy analysis (RDA), catchment land use explained 20.3% of the variance in the measured water chemistry. Agriculture had the strongest influence on the water quality of the study sites, capturing 13.1% of the variance. Nitrogen seemed to be strongly related to agriculture, whereas phosphorus was correlated with urban areas and industry. Higher than average nutrient concentrations regularly occurred at the mouths of large rivers, or close to human settlement, emphasising the significance of local sources to the nutrient concentrations of coastal waters. No increasing trend in nutrient or chlorophyll-a concentrations was observed from west to east in these shallow and sheltered nearshore areas. This contrasts with earlier results from pelagic samplings that report a marked influence of the River Neva and St. Petersburg on the nutrient status of the Gulf of Finland. Because these shallow embayments are strongly influenced by the local nutrient load, continued measures must be undertaken to reduce the nutrient load from land to prevent the continued deterioration and eutrophication of the nearshore, coastal waters.     

Total and regional body adiposity increases during menopause—evidence from a follow‐up study

For women, menopausal transition is a time of significant hormonal changes, which may contribute to altered body composition and regional adipose tissue accumulation. Excess adiposity, and especially adipose tissue accumulation in the central body region, increases women''s risk of cardiovascular and metabolic conditions and affects physical functioning. We investigated the associations between menopausal progression and total and regional body adiposity measured with dual‐energy X‐ray absorptiometry and computed tomography in two longitudinal cohort studies of women aged 47–55 (n = 230 and 148, mean follow‐up times 1.3 ± 0.7 and 3.9 ± 0.2 years, mean baseline BMI 25.5 kg/m²). We also examined associations between menopausal progression and skeletal muscle fiber characteristics, as well as adipose tissue‐derived adipokines. Relative increases of 2%–14% were observed in regional and total body adiposity measures, with a pronounced fat mass increase in the android area (4% and 14% during short‐ and long‐term follow‐ups). Muscle fiber oxidative and glycolytic capacities and intracellular adiposity were not affected by menopause, but were differentially correlated with total and regional body adiposity at different menopausal stages. Menopausal progression and regional adipose tissue masses were positively associated with serum adiponectin and leptin, and negatively associated with resistin levels. Higher diet quality and physical activity level were also inversely associated with several body adiposity measures. Therefore, healthy lifestyle habits before and during menopause might delay the onset of severe metabolic conditions in women.     

Responses of Baltic Sea Ice and Open-Water Natural Bacterial Communities to Salinity Change

To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0°C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the α- and γ-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure.     

Ultrastructural changes arising from freezing of leaf blade cells of rye (Secale cereale): an investigation using freeze-substitution

The survival at sub-zero temperatures of leaf blade cells of rye ( Secale cereale L. cv. Voima), which had not been cold acclimated, was determined by measuring the efflux of ninhydrin-positive substances: 50% of the cells were dead at −4°C (LT₅₀) and none survived at −12°C or below. Examination of ultrastructural changes during cold hardening and freezing injury requires frozen tissues prepared for transmission electron microscopy without thawing. Specimens were prepared from leaf blade segments at room temperature, −4°C or −12°C by plunge freezing at 3 m s⁻¹ into a cooling medium at −170°C followed by freeze-substitution in acetone with OsO₄ fixation. Comparisons of room temperature specimens were made with those prepared by chemical fixation using glutaraldehyde/paraformaldehyde/tannic acid. On freezing to −12°C, the cells were severely dehydrated and distorted, the vacuoles severely shrunken and the cytoplasm and mitochondria disorganized whereas the chloroplasts were little affected. On freezing to −4°C, some cells were as disorganized as those at −12°C, others were relatively intact, and some showed evidence of intracellular ice crystal formation.