We developed and tested a set of oligonucleotide primers for the specific amplification of 16S rRNA gene segments from cyanobacteria and plastids by PCR. PCR products were recovered from all cultures of cyanobacteria and diatoms that were checked but not from other bacteria and archaea. Gene segments selectively retrieved from cyanobacteria and diatoms in unialgal but nonaxenic cultures and from cyanobionts in lichens could be directly sequenced. In the context of growing sequence databases, this procedure allows rapid and phylogenetically meaningful identification without pure cultures or molecular cloning. We demonstrate the use of this specific PCR in combination with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities.

Scytonemin, the yellow‐brown pigment of cyanobacterial (blue‐green algal) extracellular sheaths, was found in species thriving in habitats exposed to intense solar radiation. Scytonemin occurred predominantly in sheaths of the outermost parts or top layers of cyanobacterial mats, crusts, or colonies. Scytonemin appears to be a single compound identified in more than 30 species of cyanobacteria from cultures and natural populations. It is lipid soluble and has a prominent absorption maximum in the near‐ultraviolet region of the spectrum (384 nm in acetone; ca. 370 nm in vivo) with a long tail extending to the infrared region. Microspectrophotometric measurements of the transmittance of pigmented sheaths and the quenching of ultraviolet excitation of phycocyanin fluorescence demonstrate that the pigment was effective in shielding the cells from incoming near‐ultraviolet‐blue radiation, but not from green or red light. High light intensity (between 99 and 250 μmol photon · m−2· S−1, depending on species) promoted the synthesis of scytonemin in cultures of cyanobacteria. In cultures, high light intensity caused reduction in the specific content of Chl a and phycobilins, increase in the ratio of total carotenoids to Chl a, and scytonemin increase. UV‐A (320–400 nm) radiation was very effective in eliciting scytonemin synthesis. Scytonemin production was physiological and not due to a mere photochemical conversion. These results strongly suggest that scytonemin production constitutes an adaptive strategy of photoprotection against short‐wavelength solar irradiance.

We compared the community structures of cyanobacteria in four biological desert crusts from Utah's Colorado Plateau developing on different substrata. We analyzed natural samples, cultures, and cyanobacterial filaments or colonies retrieved by micromanipulation from field samples using microscopy, denaturing gradient gel electrophoresis, and sequencing of 16S rRNA genes. While microscopic analyses apparently underestimated the biodiversity of thin filamentous cyanobacteria, molecular analyses failed to retrieve signals for otherwise conspicuous heterocystous cyanobacteria with thick sheaths. The diversity found in desert crusts was underrepresented in currently available nucleotide sequence databases, and several novel phylogenetic clusters could be identified. Morphotypes fitting the description of Microcoleus vaginatus Gomont, dominant in most samples, corresponded to a tight phylogenetic cluster of probable cosmopolitan distribution, which was well differentiated from other cyanobacteria traditionally classified within the same genus. A new, diverse phylogenetic cluster, named "Xeronema," grouped a series of thin filamentous Phormidium-like cyanobacteria. These were also ubiquitous in our samples and probably correspond to various botanical Phormidium and Schizothrix spp., but they are phylogenetically distant from thin filamentous cyanobacteria from other environments. Significant differences in community structure were found among soil types, indicating that soil characteristics may select for specific cyanobacteria. Gypsum crusts were most deviant from the rest, while sandy, silt, and shale crusts were relatively more similar among themselves.

Global warming will likely force terrestrial plant and animal species to migrate toward cooler areas or sustain range losses; whether this is also true for microorganisms remains unknown. Through continental-scale compositional surveys of soil crust microbial communities across arid North America, we observed a latitudinal replacement in dominance between two key topsoil cyanobacteria that was driven largely by temperature. The responses to temperature of enrichment cultures and cultivated strains support this contention, with one cyanobacterium (Microcoleus vaginatus) being more psychrotolerant and less thermotolerant than the other (M. steenstrupii). In view of our data and regional climate predictions, the latter cyanobacterium may replace the former in much of the studied area within the next few decades, with unknown ecological consequences for soil fertility and erodibility.

Despite knowledge of the existence of the pigment called scytonemin for over 100 years, its structure has remained unsolved until now. This pigment, the first shown to be an effective, photo-stable ultraviolet shield in prokaryotes, is a novel dimeric molecule (molec. wt. 544) of indolic and phenolic subunits and is known only from the sheaths enclosing the cells of cyanobacteria. It is probable that scytonemin is formed from a condensation of tryptophan- and phenylpropanoid-derived subunits. The linkage between these units is unique among natural products and this novel ring structure is here termed the 'scytoneman skeleton'. Scytonemin absorbs strongly and broadly in the spectral region 325-425 nm (UV-A-violet-blue, with an in vivo maximum at 370 nm). However, there is also major absorption in the UV-C (lambda max = 250 nm) and UV-B (280-320 nm). The pigment has been recently shown to provide significant protection to cyanobacteria against damage by ultraviolet radiation. The pigment occurs in all phylogenetic lines of sheathed cyanobacteria and possibly represents a UV screening strategy far more ancient than that of plant flavonoids and animal melanins. How diverse organisms deal with UV radiation is considered of vital importance to global ecology.

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The proposed photoprotective role of the UV-A absorbing, extracellular pigment scytonemin was studied in the terrestrial cyanobacterium Chlorogloeopsis sp. strain O-89-Cgs(1). UV-A (315-400 nm) caused growth delay, cell growth restarting only when scytonemin had accumulated in the extracellular envelopes. Cultures with scytonemin were more resistant to photoinhibition of photosynthesis than cultures without scytonemin, the differential resistance being much greater to UV-A-caused photoinhibition than to photoinhibition caused by visible light. The presence of scytonemin in the extracellular envelopes was correlated with the inability of UV-A radiation to induce strong photopigment fluorescence (685 nm emission), regardless of the specific content os photosynthetic pigments. The physical removal of the scytonemin containing extracellular envelopes brought about the loss of UV-A resistance as measured by photobleaching rates of chlorophyll a under conditions of physiological inactivity (desiccation). These observations provide strong evidence for the proposed protective role of scytonemin, as a passive UV-A sunscreen, in cyanobacteria.

We examined the morphology, physiology, and 16S rRNA gene sequences of three culture collection strains and of ten novel isolates of unicellular cyanobacteria from hypersaline environments. The strains were morphologically diverse, with average cell widths ranging from 2.8 to 10.3 micron. There were single-celled, colonial, and baeocyte-forming strains. However, morphological traits were markedly variable with culture conditions. In contrast, all strains displayed extreme halotolerance (growing close to optimally at above 12% salinity); all were obligately marine, euryhaline, and moderately thermophilic; and all shared a suite of chemotaxonomic markers including phycobilins, carotenoids, and mycosporine-like amino acids. 16S rRNA gene sequence analysis indicated that the strains were related to each other. Sequence similarity analysis placed the strains in a monophyletic cluster (which we named the Halothece cluster) apart from all cultured or uncultured, not extremely halotolerant cyanobacteria whose 16S rRNA gene sequences are available in public nucleotide sequence databases. This represents the first case in which a phylogenetically coherent group of cyanobacteria can be defined on the basis of physiology. The Halothece cluster contained two subclusters that may be divergent at the generic level, one encompassing 12 strains (spanning 5% 16S rRNA gene sequence divergence and named the Euhalothece subcluster), and a single deep-branching isolate. Phenotypic characterization of the isolates, including morphological, physiological, and chemotaxonomic traits, did not distinguish these subclusters and only weakly suggested the existence of two separate clades, one encompassing strains of small cell size (cell width < 5 m) and another one encompassing strains of larger cell size.