Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov.
Abstract
:1. Introduction
2. Material and Methods
2.1. Genome Sequences Used in this Study
2.2. Genomic DNA Extraction and Sequencing
2.3. Whole Genome Comparison
3. Results and Discussion
3.1. Genomes of Ectothiorhodospiraceae
3.2. Genomes of Halorhodospira Species
3.3. Genome-Delineated Properties
3.3.1. Sulfur and Thiosulfate Oxidation
3.3.2. Glutathione
3.3.3. Carboxysome Genes
3.3.4. Nitric Oxide Reduction
3.3.5. HIPIP
3.3.6. Cytochrome b5
3.3.7. Arsenic Oxidation
3.3.8. Photoactive Yellow Protein—PYP
3.3.9. Photosynthesis Gene Clusters
3.4. Habitats and Environmental Distribution
4. Systematic Conclusions
5. Emended Description of the Family Ectothiorhodospiraceae Imhoff 1984a, 33VP
6. Description of the Family Halorhodospiraceae. fam. nov.
6.1. Emended Description of the Genus Halorhodospira
6.2. Description of the Genus Halochlorospira gen. nov.
6.3. Description of Halochlorospira halochloris comb. nov.
6.4. Descrition of Halochlorospira abdelmalekii comb. nov.
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genome Name | Strain | Alternate Strain | Type Strain | GenBank Accessions | Contigs | Genome Length | GC mol% | quinone | CDS | Coarse Consis-tency | Fine Consis-tency | Sequencing Depth | Reference |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ectothiorhodospira haloalkaliphila | ATCC 51935 | yes | AJUE00000000 | 36 | 3,445,226 | 63.0 | MK-7/Q-8 | 3155 | 95.3 | 93.9 | Unknown | [20] | |
Ectothiorhodospira haloalkaliphila | 9902 | strain C | no | JAJNQR000000000 | 243 | 3,666,279 | 62.7 | 3602 | 95.4 | 93.7 | 106x | this study | |
Ectothiorhodospira variabilis | DSM 21381 | WN 22 | yes | JAJNAO000000000 | 84 | 3,416,336 | 63.0 | 3250 | 94.3 | 92.8 | 119x | this study | |
Ectothiorhodospira variabilis | WN 21Y | no | JAJNAP000000000 | 84 | 3,452,695 | 63.0 | 3302 | 94.3 | 92.9 | 145x | this study | ||
Ectothiorhodospira variabilis | WN 21R | no | JAJNAQ000000000 | 71 | 3,484,384 | 63.0 | 3341 | 94.3 | 92.9 | 119x | this study | ||
Ectothiorhodospira variabilis | WN 2R | no | JAJNAR000000000 | 73 | 3,484,893 | 63.0 | 3341 | 94.3 | 92.9 | 132x | this study | ||
Ectothiorhodospira sp. | BSL-9 | no | CP011994 | 1 | 3,550,080 | 63.0 | 3350 | 95.7 | 93.1 | 298x | [21] | ||
Ectothiorhodospira sp. | 9100 | YC6.1 | no | JAJNAN000000000 | 161 | 3,238,183 | 62.3 | 3169 | 93.3 | 92 | 103x | this study | |
Ectothiorhodospira sp. | 9905 | no | JAJNAM000000000 | 180 | 3,202,442 | 62.3 | 3120 | 94.8 | 93.4 | 52x | this study | ||
Ectothiorhodospira marina | DSM 241 | 9914 | yes | FOAA00000000 | 41 | 3,185,852 | 62.3 | MK-7/Q-8 | 3059 | 94.8 | 93.9 | 378x | [17] |
Ectothiorhodospira mobilis | DSM 237 | yes | NRSK01000000 | 119 | 2,796,053 | 68.3 | MK-7/Q-8 | 2714 | 95.4 | 93.1 | 539x | [17] | |
Ectothiorhodospira marismortui | DSM 4180 | 9410 | yes | FOUO00000000 | 35 | 2,624,954 | 68.2 | MK-7/Q-8 | 2474 | 94.6 | 93.7 | 363x | [17] |
Ectothiorhodospira marismortui | DG9 | no | JAJOZD000000000 | 40 | 2,682,160 | 68.4 | 2522 | 94.7 | 93.7 | 139x | this study | ||
Ectothiorhodospira vacuolata | DSM 2111 | Beta 1 | yes | JAJMLZ000000000 | 40 | 3,341,893 | 63.4 | MK-7/Q-7 | 3100 | 93.7 | 92.5 | 125x | this study |
Ectothiorhodospira sp. | PHS-1 | no | AGBG00000000 | 114 | 2,943,210 | 63.7 | 2725 | 95.6 | 94.2 | 42x | [19] | ||
Ectothiorhodospira shaposhnikovii | DSM 243 | 9710 | yes | NRSM01000000 | 154 | 3,788,226 | 62.4 | MK-7/Q-7 | 3743 | 96 | 93.9 | 160x | [17] |
Ectothiorhodospira sp. | A-7R | no | JAJNQO000000000 | 47 | 3,282,361 | 63.0 | 3009 | 96.1 | 94.4 | 84x | this study | ||
Ectothiorhodospira sp. | A-7Y | no | JAJNQN000000000 | 50 | 3,282,916 | 63.0 | 3019 | 95.9 | 94.3 | 52x | this study | ||
Ectothiorhodospira sp. | B14B | no | JAJNQM000000000 | 164 | 3,422,169 | 62.9 | 3209 | 95.5 | 93 | 10x | this study | ||
Ectothiorhodospira magna | DSM 22250 | B7-7 | yes | FOFO00000000 | 58 | 2,721,342 | 60.9 | 2559 | 94.7 | 93.6 | 438x | [17] | |
Ectothiorhodosinus mongolicus | DSM15479 | M9 | yes | FTPK00000000 | 6 | 1,990,961 | 55.6 | 1867 | 95.2 | 94.5 | 593x | [17] | |
Thiorhodospira sibirica | ATCC 700588 | yes | AGFD00000000 | 186 | 3,188,869 | 56.7 | 2842 | 93 | 92.1 | 30x | [18] | ||
Halorhodospira abdelmalekii | DSM 2110 | yes | NRRN01000000 | 158 | 3,090,835 | 62.9 | MK-4 | 2914 | 94.4 | 93.2 | 122x | [17] | |
Halorhodospira halochloris | DSM 1059 | 9850 | yes | AP017372 | 1 | 2,819,782 | 55.8 | MK-4 | 2699 | 94.4 | 93.7 | 123x | [23] |
Halorhodospira halochloris | 9851 | no | JAJNRA000000000 | 141 | 2,883,546 | 56.1 | MK-4 | 2847 | 94.1 | 93.3 | 136x | this study | |
Halorhodospira halochloris | 9852 | no | JAJNRB000000000 | 188 | 2,888,425 | 56.1 | 2861 | 93.6 | 92.8 | 91x | this study | ||
Halorhodospira neutriphila | DSM 15116 | yes | NRSH01000000 | 287 | 2,394,163 | 72.0 | 2535 | 95.5 | 92.3 | 46x | [17] | ||
Halorhodospira halophila | DSM 244 | SL1 | yes | CP000544 | 1 | 2,678,452 | 68.0 | MK-8 | 2414 | 99.7 | 99.3 | Unknown | [22] |
Halorhodospira halophila | 9630 | no | NRRO00000000 | 45 | 2,682,427 | 67.9 | MK-8 | 2522 | 99.6 | 98.9 | 220x | [17] | |
Halorhodospira halophila | 9620 | no | NHSE01000000 | 99 | 2,703,685 | 68.4 | 2600 | 99.2 | 98.3 | 49x | [17] | ||
Halorhodospira halophila | 9621 | no | JAJNRD000000000 | 87 | 2,912,850 | 67.9 | 2705 | 99.6 | 99 | 70x | this study | ||
Halorhodospira halophila | 9622 | no | JAJNRE000000000 | 121 | 2,909,722 | 67.9 | 2776 | 99.6 | 99 | 80x | this study | ||
Halorhodospira halophila | 9624 | no | JAJNRC000000000 | 20 | 2,779,891 | 68.1 | MK-8 | 2599 | 97.6 | 96.6 | 117x | this study | |
Halorhodospira halophila | 9626 | no | NHSN01000000 | 45 | 2,857,375 | 68.2 | 2720 | 99.5 | 98.9 | 72x | [17] | ||
Halorhodospira halophila | 9628 | no | JAJNRF000000000 | 27 | 2,787,144 | 68.1 | 2598 | 99.4 | 99 | 68x | this study | ||
Halorhodospira halophila | M38 | no | JAJNQP000000000 | 101 | 2,748,046 | 68.3 | 2572 | 99.4 | 98.8 | 143x | this study | ||
Halorhodospira halophila | M39old | no | JAJNQQ000000000 | 105 | 2,747,719 | 68.3 | 2571 | 99.4 | 98.8 | 135x | this study |
Ect. vacuolata DSM 2111 | |||||||||||||||||||
96.3 | Ect. PHS-1 | ||||||||||||||||||
90.5 | 90.3 | Ect. shaposhnikovii DSM 243 | |||||||||||||||||
89.4 | 89.1 | 88.1 | Ect. B14B | ||||||||||||||||
89.2 | 88.7 | 87.8 | 99 | Ect. A-7Y | |||||||||||||||
88.9 | 88.7 | 87.8 | 99.1 | 99.9 | Ect. A-7R | ||||||||||||||
86.2 | 85.9 | 84.6 | 83.4 | 83.3 | 83.6 | Ect. magna DSM 22250 | |||||||||||||
76.8 | 76.8 | 76.5 | 76.4 | 76.4 | 76.5 | 76 | Ect. BSL-9 | ||||||||||||
76.7 | 76.6 | 76.4 | 76 | 76.1 | 76.3 | 75.9 | 91.5 | Ect. haloalkaliphila ATCC 51935 | |||||||||||
76.5 | 76.5 | 76.2 | 76 | 76.1 | 76.1 | 76 | 91.3 | 98 | Ect. haloalkaliphila 9902 | ||||||||||
76.6 | 76.6 | 76.6 | 75.9 | 76 | 76.2 | 75.8 | 91.2 | 98.3 | 98.2 | Ect. variabilis WN 22 | |||||||||
76.1 | 76.1 | 76 | 75.7 | 75.9 | 76.1 | 75.5 | 86.9 | 86.8 | 86.8 | 86.6 | Ect. marina DSM 241 | ||||||||
76 | 76.3 | 75.6 | 75.5 | 75.7 | 75.9 | 75.5 | 87.3 | 86.9 | 86.8 | 86.7 | 96.7 | Ect. YC6.1 | |||||||
75.9 | 76.1 | 75.7 | 75.7 | 75.7 | 75.8 | 75.5 | 87.2 | 86.8 | 86.8 | 86.7 | 96.8 | 99.9 | Ect. 9905 | ||||||
76 | 75.8 | 75.4 | 75.1 | 75 | 75.3 | 74.9 | 76.7 | 76.2 | 76.3 | 75.9 | 76.1 | 75.9 | 75.9 | Ect. mobilis DSM 237 | |||||
75.9 | 75.8 | 75.4 | 75 | 75 | 75.3 | 74.9 | 76.7 | 76.4 | 76.4 | 76.1 | 76.1 | 76 | 76 | 92.6 | Ect. marismortui DSM 4180 | ||||
75.5 | 75.7 | 75 | 75 | 75 | 75.3 | 74.9 | 76.2 | 75.9 | 76.2 | 75.9 | 76 | 76 | 76 | 92.8 | 98 | Ect. marismortui DG9 | |||
70 | 70 | 69.8 | 69.9 | 69.8 | 69.9 | 69.9 | 70.2 | 70.2 | 70.1 | 70.1 | 70.1 | 70 | 70 | 69.5 | 69.3 | 69.5 | Ets. mongolicus DSM 15479 | ||
69.9 | 69.8 | 69.8 | 69.7 | 69.5 | 69.7 | 70 | 69.5 | 69.3 | 69.3 | 69.3 | 69.2 | 69.5 | 69.4 | 69.5 | 69.3 | 69.2 | 68.3 | Trs. siberica ATCC700588 |
Hlr. halophila SL1 | |||||||||||||||
99.99 | Hlr. halophila BN9630 | ||||||||||||||
85.8 | 85.8 | Hlr. halophila BN9626 | |||||||||||||
85.8 | 85.8 | 98 | Hlr. halophila BN9620 | ||||||||||||
85.7 | 85.7 | 98.5 | 98.1 | Hlr. halophila BN9628 | |||||||||||
85.7 | 85.7 | 98.5 | 98.1 | 100 | Hlr. halophila BN9624 | ||||||||||
85.7 | 85.7 | 98.1 | 98.5 | 98.4 | 98.4 | Hlr. halophila BN9622 | |||||||||
85.7 | 85.7 | 98.2 | 97.9 | 98.7 | 98.7 | 98.1 | Hlr. halophila BN9621 | ||||||||
85.6 | 85.5 | 97.4 | 97.9 | 97.4 | 97.4 | 98 | 97.3 | Hlr. halophila M39old | |||||||
85.6 | 85.5 | 97.3 | 97.8 | 97.4 | 97.4 | 98 | 97.3 | 100 | Hlr. halophila M38 | ||||||
77.4 | 77.4 | 77.4 | 77.4 | 77.6 | 77.6 | 77.6 | 77.6 | 77.7 | 77.6 | Hlr. neutriphila DSM 15116 | |||||
73.3 | 73.3 | 73.7 | 73.7 | 73.6 | 73.6 | 73.6 | 73.5 | 73.4 | 73.4 | 74.2 | Hlr. abdelmalekii BN9840 | ||||
70.6 | 70.5 | 70.9 | 71.1 | 71.2 | 71.2 | 71.3 | 71 | 70.8 | 70.8 | 70.7 | 72.7 | Hlr. halochloris BN9852 | |||
70.6 | 70.5 | 70.7 | 70.9 | 71 | 71 | 71 | 70.2 | 70.7 | 70.8 | 70.7 | 72.5 | 97.6 | Hlr. halochloris BN9850 | ||
70.5 | 70.4 | 70.7 | 71 | 70.9 | 70.9 | 70.8 | 71 | 70.7 | 70.8 | 70.6 | 72.5 | 97.6 | 99.94 | Hlr halochloris BN9851 |
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Imhoff, J.F.; Kyndt, J.A.; Meyer, T.E. Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov. Microorganisms 2022, 10, 295. https://doi.org/10.3390/microorganisms10020295
Imhoff JF, Kyndt JA, Meyer TE. Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov. Microorganisms. 2022; 10(2):295. https://doi.org/10.3390/microorganisms10020295
Chicago/Turabian StyleImhoff, Johannes F., John A. Kyndt, and Terrance E. Meyer. 2022. "Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov." Microorganisms 10, no. 2: 295. https://doi.org/10.3390/microorganisms10020295
APA StyleImhoff, J. F., Kyndt, J. A., & Meyer, T. E. (2022). Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov. Microorganisms, 10(2), 295. https://doi.org/10.3390/microorganisms10020295