Rosmarie Rippka

Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria

Summary: On the basis of a comparative study of 178 strains of cyanobacteria, representative of this group of prokaryotes, revised definitions of many genera are proposed. Revisions are designed to permit the generic identification of cultures, often difficult through use of the field-based system of phycological classification. The differential characters proposed are both constant and readily determinable in cultured material. The 22 genera recognized are placed in five sections, each distinguished by a particular pattern of structure and development. Generic descriptions are accompanied by strain histories, brief accounts of strain properties, and illustrations; one or more reference strains are proposed for each genus. The collection on which this analysis was based has been deposited in the American Type Culture Collection, where strains will be listed under the generic designations proposed here.

Isolation and purification of cyanobacteria.

Publisher Summary This chapter focuses on the isolation and purification of Cyanobacteria. Cyanobacterial populations recognized in their natural habitat should be sampled with sterile instruments and placed in sterile containers to ensure the origin of eventual isolates. If funds permit, commercial sterile disposable scalpels, pipets, and plastic tubes are very convenient for this purpose. Only small quantities (a pea-size equivalent generally being ample) are required from habitats where macroscopic growth is visible. Sampling of endosymbiotic cyanobacteria from coralloid nodules of Cycadaceae or the stems of Gunnera can be performed as described for soil and rock-borne cyanobacteria, but other host-cyanobacteria associations might require more special treatments. To isolate cyanobacteria from lakes and ponds in which cyanobacterial growth is not visible with the eye (or even after examination with a portable microscope) it is advisable to take larger samples: 250- to 500-ml sterile screw-cap centrifuge pots, filled almost completely with sampling water, are convenient containers for transport and allow immediate concentration (by centrifugation) on arrival in the laboratory, the sampling volume generally being sufficient to isolate cyanobacteria present even in only low numbers. The origin of many cyanobacteria currently in culture is poorly characterized because little more is known about their habitat than that they were derived from a soil sample, freshwater, or marine environment, which is rather restricted information (although better than source unknown, another not uncommon description).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for “green” biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

A cyanobacterium which lacks thylakoids

Gloebacter violaceus gen. and sp. n. is a unicellular photosynthetic prokaryote of unusual cellular structure. The only unit membrane in the small, rod-shaped cells is the cytoplasmic membrane, which has a simple contour, without intrusions. Immediately underlying it is an electron-dense layer 80 nm thick. Gloeobacter is an aerobic photoautotroph which contains chlorophyll α, β-carotene and other carotenoids, allophycocyanin, phycocyanin and phycoerythrin. Chlorophyll and carotenoids are associated with the particulate fraction of cell-free extracts, and are thus probably localized in the cytoplasmic membrane. The phycobiliproteins may be associated with the electron-dense 80 nm layer. The DNA contains 64.4 moles percent GC. The cellular lipids have a high content of polyunsaturated fatty acids, largely linoleate and γ-linolenate. Despite its atypical fine structure, Gloeobacter is evidently a cyanobacterium, sufficiently different from other unicellular cyanobacteria to be placed in a new genus.

Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides

An in situ hybridization method was applied to the identification of marine cyanobacteria assignable to the genus Prochlorococcus using horseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA). With this method very bright signals were obtained, in contrast to hybridizations with oligonucleotides monolabelled with fluorochromes, which failed to give positive signals. Genotype-specific oligonucleotides for high light (HL)- and low light (LL)-adapted members of this genus were identified by 16S rRNA sequence analyses and their specificities confirmed in whole-cell hybridizations with cultured strains of Prochlorococcus marinus Chisholm et al., 1992, Prochlorococcus sp. and Synechococcus sp. In situ hybridization of these genotype-specific probes to field samples from stratified water bodies collected in the North Atlantic Ocean and the Red Sea allowed a rapid assessment of the abundance and spatial distribution of HL- and LL-adapted Prochlorococcus. In both oceanic regions the LL-adapted Prochlorococcus populations were localized in deeper water whereas the HL-adapted Prochlorococcus populations were not only distinct in each region but also exhibited strikingly different depth distributions, HLI being confined to shallow water in the North Atlantic, in contrast to HLII, which was present throughout the water column in the Red Sea.

Phylum BX. Cyanobacteria

The oxygenic photosynthetic procaryotes comprise a single taxonomic and phylogenetic group (see master phylogenetic tree of the Bacteria). In the last edition of the Manual, two separate groups were described, but it is now apparent that members of the Prochlorales simply represent different, unrelated genera which fall into the main cluster of the Cyanobacteria (see Oxygenic Photosynthetic Bacteria, below). The principal character that defines all of these oxygenic photosynthetic procaryotes is the presence of two photosystems (PSII and PSI) and the use of H2O as the photoreductant in photosynthesis. Although facultative photo- or chemo-heterotrophy may occur in some species or strains, all known members are capable of photoautotrophy (using CO2 as the primary source of cell carbon).

Genome Size of Cyanobacteria

Summary: The genome sizes of 128 strains of cyanobacteria, representative of all major taxonomic groups, lie in the range 1.6 × 109 to 8.6 × 109 daltons. The majority of unicellular cyanobacteria contain genomes of 1.6 × 109 to 2.7 × 109 daltons, comparable in size to those of other bacteria, whereas most pleurocapsalean and filamentous strains possess larger genomes. The genome sizes are discontinuously distributed into four distinct groups which have means of 2.2 × 109, 3.6 × 109, 5.0 × 109 and 7.4 × 109 daltons. The data suggest that genome evolution in cyanobacteria occurred by a series of duplications of a small ancestral genome, and that the complex morphological organization characteristic of many cyanobacteria may have arisen as a result of this process.

Deoxyribonucleic Acid Base Composition of Cyanobacteria

Summary: The DNA base compositions of 176 strains of cyanobacteria were determined by thermal denaturation or by CsCl density gradient centrifugation. A summary of all data now available for this prokaryotic group is presented and the taxonomic and evolutionary implications are discussed.

Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.

[2] Recognition and identification of cyanobacteria

Publisher Summary This chapter focuses on the recognition and identification of Cyanobacteria. The recognition of cyanobacteria in the natural habitat is a prerequisite for their isolation, and, to isolate more particular members, it helps to know their ecological distribution. Following successful isolation, cyanobacteria (as other organisms) should be identified by a name, which serves as an indicator of the respective phenotypic properties and is therefore crucial for scientific communication. Unless the organisms have not been previously described, their names have to be chosen from an existing system of classification. As cyanobacteria were first recognized more than 150 years ago, a bewildering array of genera and species has been created by botanists and ecologists. Classifications were based either on the properties observable on samples collected from the natural habitat or on those extractable from dried herbarium specimens. Furthermore, many genera and species underwent repeated taxonomic revisions, leading to a large number of synonyms that only botanical experts are capable of unraveling. Cyanobacteria occupy a rather wide range of illuminated niches in terrestrial, freshwater, marine, and hypersaline environments, where they often occur in such abundance that they are readily visible by eye.