ECB-ART-49108
Microb Genom
2021 Jun 01;76:. doi: 10.1099/mgen.0.000595.
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Comparative genomic insights into culturable symbiotic cyanobacteria from the water fern Azolla.
Pratte BS
,
Thiel T
.
Abstract
Species of the floating, freshwater fern Azolla form a well-characterized symbiotic association with the non-culturable cyanobacterium Nostoc azollae, which fixes nitrogen for the plant. However, several cyanobacterial strains have over the years been isolated and cultured from Azolla from all over the world. The genomes of 10 of these strains were sequenced and compared with each other, with other symbiotic cyanobacterial strains, and with similar strains that were not isolated from a symbiotic association. The 10 strains fell into three distinct groups: six strains were nearly identical to the non-symbiotic strain, Nostoc (Anabaena) variabilis ATCC 29413; three were similar to the symbiotic strain, Nostoc punctiforme, and one, Nostoc sp. 2RC, was most similar to non-symbiotic strains of Nostoc linckia. However, Nostoc sp. 2RC was unusual because it has three sets of nitrogenase genes; it has complete gene clusters for two distinct Mo-nitrogenases and an alternative V-nitrogenase. Genes for Mo-nitrogenase, sugar transport, chemotaxis and pili characterized all the symbiotic strains. Several of the strains infected the liverwort Blasia, including N. variabilis ATCC 29413, which did not originate from Azolla but rather from a sewage pond. However, only Nostoc sp. 2RC, which produced highly motile hormogonia, was capable of high-frequency infection of Blasia. Thus, some of these strains, which grow readily in the laboratory, may be useful in establishing novel symbiotic associations with other plants.
PubMed ID: 34181515
PMC ID: PMC8461463
Article link: Microb Genom
Article Images: [+] show captions
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Fig. 1. Phylogenetic distance tree of genomes for the symbiotic cyanobacterial strains isolated from plants (in blue) and similar comparator strains that were not isolated from a plant (in black). Numbers at the branch points indicate bootstrap values. The value shown to the right of each strain indicates the number of genes that match a set of 74 genes identified as ‘symbiosis genes’ [34]. The criteria for a gene match are described in the Methods. Accession numbers for the ‘symbiosis’ genes of representative strains are provided in Table S3. *UCD120 has a partial copy of the gene that it is missing compared to UCD121 and UCD122. Accession numbers for these strains are provided in Table S1. Scale represents number of substitutions per site. |
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Fig. 2. Proteome amino acid identity maps based on the deduced proteins for each genome for the symbiotic cyanobacterial strains and similar comparator strains that were not isolated from a plant. (a) Strains similar to N. variabilis ATCC 29413. (b) Strains similar to N. punctiforme. (c) Strains similar to N. linckia z1. The red box in (a) indicates the absence of an 11 kb excision element in strain FSR. |
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Fig. 3. Maps of excision elements interrupting the nifD gene (in red) in the symbiotic cyanobacterial strains isolated from plants and similar comparator strains that were not isolated from a plant. The excision element in Nostoc 2RC has an 18.4 kb insertion in a gene that is a homologue of a gene in N. linckia, indicated by the red arrow. |
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Fig. 4. Maps of excision elements interrupting the hupL gene (in red) in the symbiotic cyanobacterial strain Nostoc 2RC, isolated from Azolla, and comparator strains that were not isolated from a plant. |
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Fig. 5. Maps of nif2-cnfR2 and the cnfR1-cox2 gene regions in the symbiotic cyanobacterial strain Nostoc 2RC and the comparator strain not isolated from a plant, N. variabilis. |
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Fig. 6. Phylogenetic tree of nifH/vnfH genes for the symbiotic cyanobacterial strains isolated from plants and similar comparator strains that were not isolated from a plant. The N. variabilis group represents N. variabilis ATCC 29413 and the other nearly identical strains, V5, ARAD, FSR, N2B, PNB, 9RC and YBS01, while Nostoc UCD strains represent Nostoc UCD120, UCD121 and UCD122. Accession numbers for nifH/vnfH genes are provided in Table S2. Scale represents the number of substitutions per site. |
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Fig. 7. Phylogenetic tree of vnfR genes for the cyanobacterial strains that have the structural V-nitrogenase genes (black) versus comparator strains that lack these genes (blue). The N. variabilis group represents N. variabilis ATCC 29413 and the other nearly identical strains, V5, ARAD, FSR, N2B, PNB, 9RC and YBS01. Accession numbers for vnfR genes are provided in Table S2. Scale represents the number of substitutions per site. |
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Fig. 8. Maps of fructose transport (frtABC) and glucose transport (glcP) gene regions, including genes, hrm, implicated in hormogonia regulation. |
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Fig. 9. Blasia infection and Nostoc UCD strain growth. (a) Light micrographs of uninfected Blasia auricles and Blasia auricles infected by Nostoc UCD122, N. punctiforme, N. variabilis ATCC 29413 and Nostoc 2RC. Black arrows indicate green infected auricles (about 120 μm in diameter), packed with cyanobacteria, while red arrows indicate nearly colourless uninfected auricles. Infected auricles were determined as described in the methods. (b) Liquid growth characteristics of Nostoc UCD strains. |
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Fig. 10. Phylogenetic distance tree based on genomes for representative cyanobacterial strains. ANI values are included for comparison between strains indicated by asterisks. Accession numbers for these strains are provided in Table S1. Scale represents the number of substitution per site. |
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