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.

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Generic assignments, strain histories, and properties of pure cultures of cyanobacteria

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N budget, are presented to highlight the dominant fluxes of nitrogen in each region. Important findings are that human activities increasingly dominate the N budget at the global and at most regional scales, the terrestrial and open ocean N budgets are essentially dis- connected, and the fixed forms of N are accumulating in most environmental reservoirs. The largest uncertainties in our understanding of the N budget at most scales are the rates of natural biological nitrogen fixation, the amount of Nr storage in most environmental reservoirs, and the production rates of N2 by denitrification.

/pdf/nitrogen-cycles-past-present-and-future-1zdbw0976r.pdf

Nitrogen cycles: past, present, and future

We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity. Microorganisms are responsible for most of the biogeochemical cycles that shape the environment of Earth and its oceans. Yet, these organisms are the least well understood on Earth, as the ability to study and understand the metabolic potential of microorganisms has been hampered by the inability to generate pure cultures. Recent studies have begun to explore environ

/pdf/environmental-genome-shotgun-sequencing-of-the-sargasso-sea-43wxijxylr.pdf

Environmental Genome Shotgun Sequencing of the Sargasso Sea

Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry. The probes, complementary to short sequence elements within the 16S rRNA common to phylogenetically coherent assemblages of microorganisms, were labeled with tetramethylrhodamine and hybridized to suspensions of fixed cells. Flow cytometry was used to resolve individual target and nontarget bacteria (1 to 5 microns) via probe-conferred fluorescence. Target cells were quantified in an excess of nontarget cells. The intensity of fluorescence was increased additively by the combined use of two or three fluorescent probes complementary to different regions of the same 16S rRNA. Images

Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.

For years, microbiologists characterized the Archaea as obligate extremophiles that thrive in environments too harsh for other organisms. The limited physiological diversity among cultivated Archaea suggested that these organisms were metabolically constrained to a few environmental niches. For instance, all Crenarchaeota that are currently cultivated are sulphur-metabolizing thermophiles. However, landmark studies using cultivation-independent methods uncovered vast numbers of Crenarchaeota in cold oxic ocean waters. Subsequent molecular surveys demonstrated the ubiquity of these low-temperature Crenarchaeota in aquatic and terrestrial environments. The numerical dominance of marine Crenarchaeota--estimated at 10(28) cells in the world's oceans--suggests that they have a major role in global biogeochemical cycles. Indeed, isotopic analyses of marine crenarchaeal lipids suggest that these planktonic Archaea fix inorganic carbon. Here we report the isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite--the first observation of nitrification in the Archaea. The autotrophic metabolism of this isolate, and its close phylogenetic relationship to environmental marine crenarchaeal sequences, suggests that nitrifying marine Crenarchaeota may be important to global carbon and nitrogen cycles.

/pdf/isolation-of-an-autotrophic-ammonia-oxidizing-marine-1eqf7xpo6n.pdf

Isolation of an autotrophic ammonia-oxidizing marine archaeon

The recent discovery of photosynthetic picoplankton has changed our understanding of marine food webs1. Both prokaryotic2,3 and eukaryotic4,5 species occur in most of the world's oceans and account for a significant proportion of global productivity6. Using shipboard flow cytometry, we have identified a new group of picoplankters which are extremely abundant, and barely visible using traditional microscopic techniques. These cells are smaller than the coccoid cyanobacteria and reach concentrations greater than 105 cells ml–1 in the deep euphotic zone. They fluoresce red and contain a divinyl chlorophyll a-like pigment, as well as chlorophyll b, α-carotene, and zeaxanthin. This unusual combination of pigments, and a distinctive prokaryotic ultrastructure, suggests that these picoplankters are free-living relatives of Prochloron7. They differ from previously reported prochlorophytes—the putative ancestors of the chloroplasts of higher plants—in that they contain α-carotene rather than β-carotene and contain a divinyl chlorophyll a-like pigment as the dominant chlorophyll.

A novel free-living prochlorophyte abundant in the oceanic euphotic zone

IN marked contrast to their freshwater counterparts, marine planktonic cyanobacteria are restricted to a few nostocalean genera, of which only Trichodesmium is capable of forming extensive water blooms1–3. We report here the widespread occurrence of a small, marine, chroococcalean cyanobacterium belonging to the genus Synechococcus.

Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium

Fixed nitrogen (N) often limits the growth of organisms in terrestrial and aquatic biomes, and N availability has been important in controlling the CO2 balance of modern and ancient oceans. The fixation of atmospheric dinitrogen gas (N2) to ammonia is catalysed by nitrogenase and provides a fixed N for N-limited environments. The filamentous cyanobacterium Trichodesmium has been assumed to be the predominant oceanic N2-fixing microorganism since the discovery of N2 fixation in Trichodesmium in 1961 (ref. 6). Attention has recently focused on oceanic N2 fixation because nitrogen availability is generally limiting in many oceans, and attempts to constrain the global atmosphere-ocean fluxes of CO2 are based on basin-scale N balances. Biogeochemical studies and models have suggested that total N2-fixation rates may be substantially greater than previously believed but cannot be reconciled with observed Trichodesmium abundances. It is curious that there are so few known N2-fixing microorganisms in oligotrophic oceans when it is clearly ecologically advantageous. Here we show that there are unicellular cyanobacteria in the open ocean that are expressing nitrogenase, and are abundant enough to potentially have a significant role in N dynamics.

John B. Waterbury

Papers

Generic assignments, strain histories, and properties of pure cultures of cyanobacteria

Isolation of an autotrophic ammonia-oxidizing marine archaeon

A novel free-living prochlorophyte abundant in the oceanic euphotic zone

Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium

Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean.