In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.

/pdf/the-natural-history-of-nitrogen-fixation-4970a05l9p.pdf

The Natural History of Nitrogen Fixation

Most microbial communities consist of a genetically diverse assembly of different organisms, and the level of genetic diversity plays an important part in community properties and functions. However, biological diversity also arises at a lower level of biological organization, between genetically identical cells that reside in the same microenvironment. In this Review, I outline the molecular mechanisms responsible for phenotypic heterogeneity and discuss how phenotypic heterogeneity allows genotypes to persist in fluctuating environments. I also describe how it promotes interactions between phenotypic subpopulations in clonal groups, providing microbial groups with new functionality.

A functional perspective on phenotypic heterogeneity in microorganisms

The perpetuation of symbioses through host generations relies on symbiont transmission. Horizontally transmitted symbionts are taken up from the environment anew by each host generation, and vertically transmitted symbionts are most often transferred through the female germ line. Mixed modes also exist. In this Review we describe the journey of symbionts from the initial contact to their final residence. We provide an overview of the molecular mechanisms that mediate symbiont attraction and accumulation, interpartner recognition and selection, as well as symbiont confrontation with the host immune system. We also discuss how the two main transmission modes shape the evolution of the symbiotic partners.

https://europepmc.org/articles/PMC2967712?pdf=render

A complex journey: transmission of microbial symbionts

Constraints to commercialization of algal fuels.

https://www.carey.biol.vt.edu/wp-content/uploads/2013/09/Carey_2012_Water-Res.pdf

Eco-physiological adaptations that favour freshwater cyanobacteria in a changing climate

Summary 3

I. introduction 4

II. the cyanobacteria 7

III. the heterocyst 9

1. Function and metabolism 9

2. Heterocyst structure 12

(a) Overview 12

(b) The polysaccharide (homogeneous) layer 12

(c) The glycolipid (laminated) layer 12

(d) The septum and microplasmodesmata 12

3. Nitrogen regulation and heterocyst development 12

4. Heterocyst development 13

(a) The proheterocyst 13

(b) Proteolysis associated with heterocyst development 14

(c) RNA polymerase sigma factors 14

(d) Developmental regulation of heterocyst cell wall and nitrogenase gene expression 14

(e) Genome rearrangements associated with heterocyst development 15

5. Genes essential for heterocyst development 15

(a) hetR 15

(b) Protein phosphorylation and the regulation of hetR activity 16

(c) hetR in nonheterocystous cyanobacteria 16

(d) Other heterocyst-specific genes 16

6. Heterocyst spacing 18

(a) Patterns of heterocyst differentiation 18

(b) Genes involved in heterocyst spacing 18

(c) Disruption of heterocyst pattern 18

7. Filament fragmentation and the regression of developing heterocysts 20

8. The nature of the heterocyst inhibitor 20

9. Cell selection during differentiation and pattern formation 20

(a) Cell division 20

(b) DNA replication and the cell cycle 21

(c) Competition 21

10. Models for heterocyst differentiation and pattern control 21

IV. the akinete 23

1. Properties of akinetes 23

2. Structure, composition and metabolism 24

3. Relationship to heterocysts 24

4. Factors that influence akinete differentiation 24

5. Extracellular signals 25

6. Akinete germination 25

7. Genes involved in akinete differentiation 26

V. conclusion 26

Acknowledgements 27

References 28

Cyanobacteria are an ancient and morphologically diverse group of photosynthetic prokaryotes. They were the first organisms to evolve oxygenic photosynthesis, and so changed the Earth's atmosphere from anoxic to oxic. As a consequence, many nitrogen-fixing bacteria became confined to suitable anoxic environmental niches, because the enzyme nitrogenase is highly sensitive to oxygen. However, in the cyanobacteria a number of strategies evolved that protected nitrogenase from oxygen, including a temporal separation of oxygenic photosynthesis and nitrogen fixation and, in some filamentous strains, the differentiation of a specialized cell, the heterocyst, which provided a suitable microaerobic environment for the functioning of nitrogenase. The evolution of a spore-like cell, the akinete, almost certainly preceded that of the heterocyst and, indeed, the akinete may have been the ancestor of the heterocyst. Cyanobacteria have the capacity to differentiate several additional cell and filament types, but this review will concentrate on the heterocyst and the akinete, emphasizing the differentiation and spacing of these specialized cells.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1469-8137.1999.00505.x

Tansley Review No. 107. Heterocyst and akinete differentiation in cyanobacteria

Silicified deposits, such as sinters, occur in several modern geothermal environments, but the mechanisms of silicification (and crucially the role of microorganisms in their construction) are still largely unresolved. Detailed examination of siliceous sinter, in particular sections of microstromatolites growing at the Krisuvik hot spring, Iceland, reveals that biomineralization contributes a major component to the overall structure, with approximately half the sinter thickness attributed to silicified microorganisms. Almost all microorganisms observed under the scanning electron microscope (SEM) are mineralized, with epicellular silica ranging in thickness from < 5 lm coatings on individual cells, to regions where entire colonies are cemented together in an amorphous silica matrix tens of micrometres thick. Within the overall profile, there appears to be two very distinct types of laminae that alternate repeatedly throughout the microstromatolite: ‘microbial’ layers are predominantly consisting of filamentous, intact, vertically aligned, biomineralized cyanobacteria, identified as Calothrix and Fischerella sp.; and weakly laminated silica layers which appear to be devoid of any microbial component. The microbial layers commonly have a sharply defined base, overlying the weakly laminated silica, and a gradational upper surface merging into the weakly laminated silica. These cyclic laminations are probably explained by variations in microbial activity. Active growth during spring/ summer allows the microorganisms to keep pace with silicification, with the cell surfaces facilitating silicification, while during their natural slow growth phase in the dark autumn/winter months silicification exceeds the bacteria’s ability to compensate (i.e. grow upwards). At this stage, the microbial colony is probably not essential to microstromatolite formation, with silicification presumably occurring abiogenically. When conditions once again become favourable for growth, recolonization of the solid silica surface by free-living bacteria occurs: cell motility is not responsible for the laminations. We have also observed that microbial populations within the microstromatolite, some several mm in depth, appear viable, i.e. they still have their pigmentation, the trichomes are not collapsed, cell walls are unbroken, cytoplasm is still present and they proved culturable. This suggests that the bulk of silicification occurred rapidly, probably while the cells were still alive. Surprisingly, however, measurements of light transmittance through sections of the microstromatolite revealed that photosynthetically active light (PAL) only transmitted through the uppermost 2 mm. Therefore the ‘deeper’ microbial

/pdf/microbial-silica-interactions-in-icelandic-hot-spring-sinter-1seve0o5k1.pdf

Microbial-silica interactions in Icelandic hot spring sinter: possible analogues for some Precambrian siliceous stromatolites

Cyanobacteria are a large group of photosynthetic prokaryotes of enormous environmental importance, being responsible for a large proportion of global CO 2 and N 2 fixation. They form symbiotic associations with a wide range of eukaryotic hosts including plants, fungi, sponges, and protists. The cyanobacterial symbionts are often filamentous and fix N 2 in specialized cells known as heterocysts, enabling them to provide the host with fixed nitrogen and, in the case of non-photosynthetic hosts, with fixed carbon. The best studied cyanobacterial symbioses are those with plants, in which the cyanobacteria can infect the roots, stems, leaves, and, in the case of the liverworts and hornworts, the subject of this review, the thallus. The symbionts are usually Nostoc spp. that gain entry to the host by means of specialized motile filaments known as hormogonia. The host plant releases chemical signals that stimulate hormogonia formation and, by chemoattraction, guide the hormogonia to the point of entry into the plant tissue. Inside the symbiotic cavity, host signals inhibit further hormogonia formation and stimulate heterocyst development and dinitrogen fixation. The cyanobionts undergo morphological and physiological changes, including reduced growth rate and CO 2 fixation, and enhanced N 2 fixation, and release to the plant much of the dinitrogen fixed. This short review summarizes knowledge of the cyanobacterial symbioses with liverworts and hornworts, with particular emphasis on the importance of pili and gliding motility for the symbiotic competence of hormogonia.

/pdf/cyanobacteria-bryophyte-symbioses-35cawn3woi.pdf

Cyanobacteria–bryophyte symbioses

Heterocyst-forming filamentous cyanobacteria are true multicellular prokaryotes, in which heterocysts and vegetative cells have complementary metabolism and are mutually dependent. The mechanism for metabolite exchange between cells has remained unclear. To gain insight into the mechanism and kinetics of metabolite exchange, we introduced calcein, a 623-Da fluorophore, into the Anabaena cytoplasm. We used fluorescence recovery after photobleaching to quantify rapid diffusion of this molecule between the cytoplasms of all the cells in the filament. This indicates nonspecific intercellular channels allowing the movement of molecules from cytoplasm to cytoplasm. We quantify rates of molecular exchange as filaments adapt to diazotrophic growth. Exchange among vegetative cells becomes faster as filaments differentiate, becoming considerably faster than exchange with heterocysts. Slower exchange is probably a price paid to maintain a microaerobic environment in the heterocyst. We show that the slower exchange is partly due to the presence of cyanophycin polar nodules in heterocysts. The phenotype of a null mutant identifies FraG (SepJ), a membrane protein localised at the cell–cell interface, as a strong candidate for the channel-forming protein.

/pdf/mechanism-of-intercellular-molecular-exchange-in-heterocyst-22upvmu2zk.pdf

David G. Adams

Papers

Tansley Review No. 107. Heterocyst and akinete differentiation in cyanobacteria

Microbial-silica interactions in Icelandic hot spring sinter: possible analogues for some Precambrian siliceous stromatolites

Cyanobacteria–bryophyte symbioses

Mechanism of intercellular molecular exchange in heterocyst‐forming cyanobacteria

Heterocyst formation in cyanobacteria.