Biology:Epithemia

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Epithemia is a genus of diatoms belonging to the family Rhopalodiaceae.[1] The genus has cosmopolitan distribution and are found in freshwater and marine ecosystems.[2][1] Recent studies have proposed that the genus Rhopalodia should be recategorized to join Epithemia based on phylogenetic evidence,[3] although this change in nomenclature has been disputed[4] or ignored.[5]

Members of this genus have endosymbionts that fix nitrogen called spheroid bodies, that are derived from cyanobacteria.[6][7] Because of their nitrogen fixing endosymbionts, they can be a possible indicator of eutrophication, because Epithemia abundance decreased with increased ambient inorganic N concentrations.[8]

Endosymbiosis

Epithemia and Rhopalodia, two (or one) genera of rhopalodiacean diatoms, have nitrogen-fixing endosymbioants called spheroid bodies (SBs) or diazoplasts[lower-alpha 1] in addition to the regular chloroplast and mitochondria. They are cyanobacteria that have undergone various degrees of gene loss in adaptation to their new dependent lifestyle. The SB of E. turgida has undergone faster evolution and more gene loss compared to the SB of E. gibberula.[9]

The diazoplasts have no photosynthetic genes at all.[10] They have complete OPP, C3 glycolysis, AA synthesis, and glycogen utilization pathways, but see their C6 glycolysis and TCA cycle interrupted by gene deletions. They retain thylakoid membranes. They perform nitrogen fixation in both daytime and nighttime, relying on catabolizing host-provided C3 and C6 sugars.[11]

Unlike other organelles (including the relatively recent cases of nitroplasts), the diazoplast does not have a high degree of functional gene transfer to the host's nuclear genome and has minimal reliance on host-imported proteins. Nevertheless, they display typical organelle traits of metabolic dependence on the host and coordinated division. This arrangement may suggest a way to more easily engineer nitrogen fixation into crops.[12]

Relatives

The closest relatives of the SBs are various members of the (overly broad, since divided)[13] genus Cyanothece, especially strain ATCC 51142. Based on fossil records, the symbiosis happened in a common ancestor of species that carry it about 35 million years ago.[7] The SBs are closely related to the nitroplasts,[14] which had separately entered into an endosymbiosis with Braarudosphaera bigelowii about 90 million years ago.[15]

GTDB annotates the SB of E. gibberula as Rippkaea sp003574135, a species-level cluster bearing a placeholder name.[16] Additional assignments include Ri. sp000829235 for the E. turgida SB, Ri. sp029919255 for the E. clementina SB, and Ri. sp947331815 for the E. pelagica SB.[lower-alpha 2] The closest named to the SBs is Rippkaea orientalis.[17]

For a phylogeny, see Rippkaea § Phylogeny.

Species

Those marked with a * were previously in the genus Rhopalodia.[1]

  • Epithemia adnata (Kützing) Brébisson, 1838
  • Epithemia alpestris Kützing, 1844
  • Epithemia alpestris W.Smith, 1853
  • Epithemia anasthasiae Pantocsek, 1902
  • Epithemia argus (Ehrenberg) Kützing 1844
  • Epithemia catenata[2]
  • Epithemia constricta W. Smith (Krammer)*[18]
  • Epithemia gibba Kützing, 1844*
  • Epithemia gibberula Kützing, 1844*
  • Epithemia musculus Kützing, 1844*
  • Epithemia pelagica[2]
  • Epithemia reicheltii Schmidt et al. 1904
  • Epithemia smithii Carruthers 1864
  • Epithemia sorex Kützing, 1844
  • Epithemia turgida Kützing, 1844

Phylogeny

Phylogeny of Epithemia
Source Ruck et al. (2016)[3] Moulin et al. (2024)[19]
Sequence data rbcL-psbC-cob-rDNA 18S rDNA-psbC-rbcL
Method Four MrBayes runs, majority rule Unknown
Phylogram
 

Auricula

 
 
 

Protokeelia bassonii

 
 
 
 

Rhopalodia sp.

 
 
 

Rhopalodia sp.

 
 

Rhopalodia cf. musculus

 
 
 
 
 
 

Rhopalodia iriomotensis

 
 

Rhopalodia operculata

 
 
 
 
 
 

Epithemia sorex[lower-alpha 3]

 
 

Epithemia argus

 
 
 
 

Epithemia hyndmannii

 
 
 

Epithemia sp.

 
 

Epithemia turgida[lower-alpha 3]

 
 
 
(3)
 
 
 

Rhopalodia cf. gibba

 
 

Rhopalodia gibba[lower-alpha 3]

 
 
 
 

Rhopalodia contorta

 
 
 

Rhopalodia sp.

 
 

Rhopalodia parallela

 
 
 
(4)
(2)
 
(1)
 
 

Coronia, Petrodictyon, Surirella, Iconella

 
 

Thalassiophysa hyalina 4vi08 1C1

 
 
 

Protokeelia bassonii 3564 A20

 
95
 

Auricula complexa 26vi08 1J 1

 
99
100
100
 

Epithemia catenata[lower-alpha 3] UHM3210

 
 

Rhopalodia sp. 13vi08 2B GCCT21

 
 
 

Rhopalodia sp. 3825 12

 
 
91
40
41
75
 

Epithemia clementina[lower-alpha 3]

 
 

Epithemia iriomotensis 28vi08 1C 1

 
 
 

Rhopalodia sp. 9vi08 1F 2

 
 
 

Epithemia pelagica[lower-alpha 3] UHM3202

 
 
100
100
100
 

Epithemia argus CH211

 
 

Epithemia sorex[lower-alpha 3] CH148

 
 
100
 

Epithemia hyndmannii LO320

 
100
 

Epithemia turgida CH154

 
 

Epithemia turgida CYTX021

 
[lower-alpha 3]
 
(3)
100
95
 

Rhopalodia cf. gibba nycRhop

 
100
 

Rhopalodia gibba CYTX022

 
 

Rhopalodia gibba L924

 
[lower-alpha 3]
 
67
51
 

Rhopalodia contorta L1299

 
 

Rhopalodia gibba CH155

 
 
100
 

Epithemia parallela L1370

 
 

Epithemia parallela N09 43 rhop2 3

 
 
 
(4)
(2)
 
(1)
 
 

Key to clade labels:

  1. Epithemia s.l. (post-merge sensu Ruck et al. 2016). Also the last common ancestor node of all diazoplast-carrying species.
  2. Freshwater clade
  3. Traditional Epithemia s.s.
  4. Freshwater Rhopalodia

What is traditionally known as Rhopalodia is paraphyletic to Epithemia. A merge is performed by Ruck et al. (2016) to maintain monophyly. An alternative would be to constrict Rhopalodia to the freshwater clade (which includes the type species R. gigga), moving the grade of "marine Rhopalodia" to incertae sedis. In this new view, Rhopalodia sensu stricto would be sister to Epithemia.[3]

Traditional (pre-merge) Epithemia is sister to Tetralunata according to the scientists who proposed Tetralunata.[3] Larger (post-merge) Epithemia is sister to Protokeelia, as far as the only species sampled in Ruck et al. (2016) – Protokeelia bassonii – is concerned. There is considerable uncertainty regarding the placement of Auricula.[3]

References

  1. ↑ Contrary to what the -plast suffix may imply, thee organelle are not derived from the original plastid.
  2. ↑ Mapping from provisional names of diazoplasts to published names of Epithemia hosts is obtained as follows: the associated NCBI genome assembly records is queried based on the GTDB genome IDs (e.g. GCF_003574135.1) and the host species name is found from the linked publication or BioSample metadata.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 Has diazoplast. NCBI txid 2841584 (adnata), 2809052 (catenata), 3034674 (clementina), 2809053 (pelagica), 718215 (sorex), 718217 (turgida), 3418554 (fuxianensis), 309035 (gibba), 1763363 (gibberula), 3418553 (inflata), 3455944 (musculus), 3420184 (sterrenbergii), 3418552 (yunnanensis).
  1. ↑ 1.0 1.1 1.2 "Epithemia F.T.Kützing, 1844" (in en). https://www.gbif.org/species/2637428. 
  2. ↑ 2.0 2.1 2.2 Schvarcz, Christopher R.; Wilson, Samuel T.; Caffin, Mathieu; Stancheva, Rosalina; Li, Qian; Turk-Kubo, Kendra A.; White, Angelicque E.; Karl, David M. et al. (2022-02-10). "Overlooked and widespread pennate diatom-diazotroph symbioses in the sea" (in en). Nature Communications 13 (1): 799. doi:10.1038/s41467-022-28065-6. ISSN 2041-1723. PMID 35145076. Bibcode: 2022NatCo..13..799S. 
  3. ↑ 3.0 3.1 3.2 3.3 3.4 Ruck, Elizabeth C.; Nakov, Teofil; Alverson, Andrew J.; Theriot, Edward C. (2016-10-01). "Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales". Molecular Phylogenetics and Evolution 103: 155–171. doi:10.1016/j.ympev.2016.07.023. ISSN 1055-7903. PMID 27456747. Bibcode: 2016MolPE.103..155R. 
  4. ↑ Kociolek, J.P.; Greenwood, M.; Hamsher, S.E.; Miller, S.; Li, J. (2024-04-02). "Valve ultrastructure of Rhopalodia constricta (W.Smith) Krammer (Rhopalodiales, Bacillariophyceae) and a consideration of its systematic placement" (in en). Diatom Research 39 (2): 51–60. doi:10.1080/0269249X.2024.2378769. ISSN 0269-249X. Bibcode: 2024DiaRe..39...51K. https://www.tandfonline.com/doi/full/10.1080/0269249X.2024.2378769. 
  5. ↑ Li, Kehui; Zhou, Yun; Chang, Aimee Caye G.; Amaral, Mailor W. W.; Keepers, Kyle G.; Nan, Fangru; Liu, Xudong; Wang, Jie et al. (December 2025). "Morphology, phylogeny, and organelle genomics of three new Rhopalodia species (Rhopalodiales, Bacillariophyceae)". Journal of Phycology (Wiley Periodicals Inc.) 61 (6): 1767–1784. doi:10.1111/jpy.70114. ISSN 1529-8817. PMID 41328739. 
  6. ↑ Nakayama, Takuro; Kamikawa, Ryoma; Tanifuji, Goro; Kashiyama, Yuichiro; Ohkouchi, Naohiko; Archibald, John M.; Inagaki, Yuji (2014-08-05). "Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle" (in en). Proceedings of the National Academy of Sciences 111 (31): 11407–11412. doi:10.1073/pnas.1405222111. ISSN 0027-8424. PMID 25049384. Bibcode: 2014PNAS..11111407N. 
  7. ↑ 7.0 7.1 Nakayama, Takuro; Ikegami, Yuko; Nakayama, Takeshi; Ishida, Ken-ichiro; Inagaki, Yuji; Inouye, Isao (2011-01-01). "Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium" (in en). Journal of Plant Research 124 (1): 93–97. doi:10.1007/s10265-010-0355-0. ISSN 1618-0860. PMID 20512519. Bibcode: 2011JPlR..124...93N. https://link.springer.com/article/10.1007/s10265-010-0355-0. 
  8. ↑ Stancheva, Rosalina; Sheath, Robert G.; Read, Betsy A.; McArthur, Kimberly D.; Schroepfer, Chrystal; Kociolek, J. Patrick; Fetscher, A. Elizabeth (2013-12-01). "Nitrogen-fixing cyanobacteria (free-living and diatom endosymbionts): their use in southern California stream bioassessment" (in en). Hydrobiologia 720 (1): 111–127. doi:10.1007/s10750-013-1630-6. ISSN 1573-5117. Bibcode: 2013HyBio.720..111S. 
  9. ↑ Nakayama, Takuro; Inagaki, Yuji (12 October 2017). "Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms". Scientific Reports 7 (1). doi:10.1038/s41598-017-13578-8. 
  10. ↑ Nakayama, T; Kamikawa, R; Tanifuji, G; Kashiyama, Y; Ohkouchi, N; Archibald, JM; Inagaki, Y (5 August 2014). "Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.". Proceedings of the National Academy of Sciences of the United States of America 111 (31): 11407-12. doi:10.1073/pnas.1405222111. PMID 25049384. 
  11. ↑ Moulin, SLY; Frail, S; Braukmann, T; Doenier, J; Steele-Ogus, M; Marks, JC; Mills, MM; Yeh, E (January 2024). "The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote.". ISME communications 4 (1). doi:10.1093/ismeco/ycae055. PMID 38707843. 
  12. ↑ Frail, S; Steele-Ogus, M; Doenier, J; Moulin, SLY; Braukmann, T; Xu, S; Yeh, E (19 August 2025). "Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis.". Proceedings of the National Academy of Sciences of the United States of America 122 (33). doi:10.1073/pnas.2507237122. PMID 40794833. 
  13. ↑ Mareš, J; Johansen, JR; Hauer, T; Zima J, Jr; Ventura, S; Cuzman, O; Tiribilli, B; Kaštovský, J (June 2019). "Taxonomic resolution of the genus Cyanothece (Chroococcales, Cyanobacteria), with a treatment on Gloeothece and three new genera, Crocosphaera, Rippkaea, and Zehria.". Journal of phycology 55 (3): 578-610. doi:10.1111/jpy.12853. PMID 30830691. 
  14. ↑ Cornejo‐Castillo, Francisco M.; Muñoz‐Marín, Maria del Carmen; Turk‐Kubo, Kendra A.; Royo‐Llonch, Marta; Farnelid, Hanna; Acinas, Silvia G.; Zehr, Jonathan P. (January 2019). "UCYN‐A3, a newly characterized open ocean sublineage of the symbiotic N 2 ‐fixing cyanobacterium Candidatus Atelocyanobacterium thalassa". Environmental Microbiology 21 (1): 111–124. doi:10.1111/1462-2920.14429. PMID 30255541. 
  15. ↑ Cornejo-Castillo, Francisco M.; Cabello, Ana M.; Salazar, Guillem; Sánchez-Baracaldo, Patricia; Lima-Mendez, Gipsi; Hingamp, Pascal; Alberti, Adriana; Sunagawa, Shinichi et al. (22 March 2016). "Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton". Nature Communications 7 (1). doi:10.1038/ncomms11071. 
  16. ↑ "GTDB - GCF_003574135.1". https://gtdb.ecogenomic.org/genome?gid=GCF_003574135.1. 
  17. ↑ "GTDB - Search "cyanobacterium endosymbiont"". https://gtdb.ecogenomic.org/searches?s=al&q=%22cyanobacterium%20endosymbiont%22. 
  18. ↑ Kociolek, J.P.; Greenwood, M.; Hamsher, S.E.; Miller, S.; Li, J. (2024-04-02). "Valve ultrastructure of Rhopalodia constricta (W.Smith) Krammer (Rhopalodiales, Bacillariophyceae) and a consideration of its systematic placement" (in en). Diatom Research 39 (2): 51–60. doi:10.1080/0269249X.2024.2378769. ISSN 0269-249X. Bibcode: 2024DiaRe..39...51K. https://www.tandfonline.com/doi/full/10.1080/0269249X.2024.2378769. 
  19. ↑ Moulin, SLY; Frail, S; Braukmann, T; Doenier, J; Steele-Ogus, M; Marks, JC; Mills, MM; Yeh, E (January 2024). "The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote.". ISME communications 4 (1). doi:10.1093/ismeco/ycae055. PMID 38707843. 

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