Special Issue "Genomics, Metagenomics and Phylogenomics of Cyanobacteria and Related Lineages"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (10 October 2021).

Special Issue Editors

Prof. Dr. Denis Baurain
E-Mail Website
Guest Editor
InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium
Interests: bioinformatics; databases; genetics; phylogenetics; phylogenomics; comparative genomics; protistology; plastids; Cyanobacteria
Dr. Luc Cornet
E-Mail Website
Guest Editor
Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
Interests: Cyanobacteria; genomics; metagenomics; genome assembly; NGS; TGS; palaeobiology; bacterial evolution

Special Issue Information

Dear Colleagues,

Cyanobacteria, also known as blue-green algae, are one of the most diversified groups of prokaryotes. They are of primary importance from evolutionary, ecological, biogeochemical, and industrial perspectives. Fossilized Cyanobacteria suggest that they have been present on Earth since the Proterozoic. Oxygenic photosynthesis appeared within this group at least 2.4 billion years ago, and Cyanobacteria later played a key role in the spread of photosynthesis to eukaryotes through endosymbiosis. In our age, they are still a major component of marine phytoplankton and have colonized a wide range of freshwater and terrestrial habitats. Moreover, it has recently been shown that cyanobacteria produce methane at a substantial rate, thereby raising the issue of their role in climate change. Finally, their capacity to synthesize a range of bioactive compounds makes them promising for industry (e.g., pharmaceutical companies).

From a taxonomic perspective, the cyanobacterial phylum has recently been expanded by the addition of four non-photosynthetic lineages (Melainabacteria, Sericytochromatia, Margulisbacteria, and Saganbacteria), with the side effect of renaming the traditional Cyanobacteria to Oxyphotobacteria. Of course, the pertinence of such a modification is hotly debated in the literature, with some authors insisting on the historical meaning of the name while others prefer to rely on a phylogenomic definition of the group. For all these reasons, cyanobacterial genomes are now under intense scrutiny. With the decreasing cost of next-generation sequencing and the emergence of third-generation sequencing, improving our knowledge of this phylum has never been so exciting.

In this Special Issue, we will tour the state-of-the-art in the field of genomics of Cyanobacteria and related lineages. More precisely, all manuscripts focusing on genome sequencing and assembly, genome mining and metabolic reconstruction, environmental metagenomics, phylogenomics, and software dedicated or applied to cyanobacterial genomics will be considered.

Prof. Denis Baurain
Dr. Luc Cornet
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cyanobacteria
  • genome assembly
  • genome evolution
  • phylogeny
  • comparative genomics
  • cyanobacterial evolution
  • microbial consortia
  • NRPS
  • PKS
  • database
  • genomic workflow

Published Papers (5 papers)

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Research

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Article
Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria
Genes 2021, 12(6), 929; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060929 - 18 Jun 2021
Viewed by 732
Abstract
The evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth’s history, leading eventually to the oxygenation of Earth’s atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of [...] Read more.
The evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth’s history, leading eventually to the oxygenation of Earth’s atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of aerobic respiration likely evolved after the evolution of oxygenic photosynthesis. However, complex I of the respiratory complex chain can be involved in anaerobic processes and, therefore, may have pre-dated the evolution of oxygenic photosynthesis. If so, aerobic respiration may have built upon respiratory chains that pre-date the rise of oxygen in Earth’s atmosphere. The Melainabacteria provide a unique opportunity to examine this hypothesis because they contain genes for aerobic respiration but likely diverged from the Cyanobacteria before the evolution of oxygenic photosynthesis. Here, we examine the phylogenies of translated complex I sequences from 44 recently published Melainabacteria metagenome assembled genomes and genomes from other Melainabacteria, Cyanobacteria, and other bacterial groups to examine the evolutionary history of complex I. We find that complex I appears to have been present in the common ancestor of Melainabacteria and Cyanobacteria, supporting the idea that aerobic respiration built upon respiratory chains that pre-date the evolution of oxygenic photosynthesis and the rise of oxygen. Full article
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Article
Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide
Genes 2021, 12(3), 426; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030426 - 16 Mar 2021
Viewed by 931
Abstract
Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic [...] Read more.
Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1–2 mm thick layer of 50 µmol L−1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. A metagenome-assembled genome of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, the ability of the organism to reduce Photosystem I via sulfide quinone reductase while Photosystem II is sulfide-inhibited, thereby performing anoxygenic photosynthesis in the presence of sulfide, has yet to be demonstrated. Full article
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Article
Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014
Genes 2021, 12(3), 389; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030389 - 09 Mar 2021
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Abstract
Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven [...] Read more.
Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity. Full article
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Review

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Review
Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications
Genes 2021, 12(4), 500; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12040500 - 29 Mar 2021
Cited by 1 | Viewed by 941
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for [...] Read more.
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive “omics” data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism. Full article
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Other

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Hypothesis
Are Cyanobacteria an Ancestor of Chloroplasts or Just One of the Gene Donors for Plants and Algae?
Genes 2021, 12(6), 823; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060823 - 27 May 2021
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Abstract
Chloroplasts of plants and algae are currently believed to originate from a cyanobacterial endosymbiont, mainly based on the shared proteins involved in the oxygenic photosynthesis and gene expression system. The phylogenetic relationship between the chloroplast and cyanobacterial genomes was important evidence for the [...] Read more.
Chloroplasts of plants and algae are currently believed to originate from a cyanobacterial endosymbiont, mainly based on the shared proteins involved in the oxygenic photosynthesis and gene expression system. The phylogenetic relationship between the chloroplast and cyanobacterial genomes was important evidence for the notion that chloroplasts originated from cyanobacterial endosymbiosis. However, studies in the post-genomic era revealed that various substances (glycolipids, peptidoglycan, etc.) shared by cyanobacteria and chloroplasts are synthesized by different pathways or phylogenetically unrelated enzymes. Membranes and genomes are essential components of a cell (or an organelle), but the origins of these turned out to be different. Besides, phylogenetic trees of chloroplast-encoded genes suggest an alternative possibility that chloroplast genes could be acquired from at least three different lineages of cyanobacteria. We have to seriously examine that the chloroplast genome might be chimeric due to various independent gene flows from cyanobacteria. Chloroplast formation could be more complex than a single event of cyanobacterial endosymbiosis. I present the “host-directed chloroplast formation” hypothesis, in which the eukaryotic host cell that had acquired glycolipid synthesis genes as an adaptation to phosphate limitation facilitated chloroplast formation by providing glycolipid-based membranes (pre-adaptation). The origins of the membranes and the genome could be different, and the origin of the genome could be complex. Full article
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