Planctomycetes

Planctomycetes
Scientific classification
Domain:	Bacteria
Phylum:	Planctomycetes Garrity and Holt, 2001
Families & Genera
Phycisphaerae Fukunaga et al. 2010 Phycisphaerales Fukunaga et al. 2010 Phycisphaeraceae Fukunaga et al. 2010 Phycisphaera Fukunaga et al. 2010 Planctomycetacia Cavalier-Smith 2002 Planctomycetales Schlesner and Stackebrandt 1987 ?Candidatus Nostocoida limicola III Brocadiaceae Candidatus Brocadia Jetten et al. 2001 Candidatus Kuenenia Schmid et al. 2000 Candidatus Scalindua Schmid et al. 2003 Candidatus Anammoxoglobus Kartal et al. 2006 Candidatus Jettenia Quan et al. 2008 Planctomycetaceae Schlesner and Stackebrandt 1987 Aquisphaera Bondoso et al. 2011 Blastopirellula Schlesner et al. 2004 Gemmata Franzmann and Skerman 1985 Isosphaera Giovannoni et al. 1995 Pirellula Schlesner and Hirsch 1987 emend. Schlesner et al. 2004 Planctomyces Gimesi 1924 Rhodopirellula Schlesner et al. 2004 Schlesneria Kulichevskaya et al. 2007 Singulisphaera Kulichevskaya et al. 2008 emend. Kulichevskaya et al. 2012 Telmatocola Kulichevskaya et al. 2012 Zavarzinella Kulichevskaya et al. 2009

Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, and marine and fresh water. They reproduce by budding. In structure, the organisms of this group are ovoid and have a holdfast, at the tip of a thin cylindrical extension from the cell body called the stalk, at the nonreproductive end that helps them to attach to each other during budding.

Cavalier-Smith has postulated that the Planctomycetes are within the clade Planctobacteria in the larger clade Gracilicutes, but this is not generally accepted.

Structure

For a long time bacteria belonging to this group were considered to lack peptidoglycan, (also called murein) in their cell walls, which is an important heteropolymer present in most bacterial cell walls that serves as a protective component. It was thought that instead their walls were made up of glycoprotein which is rich in glutamate. Recently, however, representatives of all three clades within the Planctomycetes were found to possess peptidoglycan containing cell walls.^[1][2]

Planctomycetes have a distinctive morphology with the appearance of membrane-bound internal compartments, often referred to as the paryphoplasm (ribosome-free space), pirellulosome (ribosome-containing space) and nucleoid (condensed nucleic acid region, in these species surrounded by a double membrane).^[3][4] Until the discovery of the Poribacteria, planctomycetes were the only bacteria known with these apparent internal compartments.^[5] Three-dimensional electron tomography reconstruction of a representative species, Gemmata obscuriglobus, has yielded varying interpretations of this observation. One 2013 study found the appearance of internal compartments to be due to a densely invaginated but continuous single membrane, concluding that only the two compartments typical of Gram-negative bacteria - the cytoplasm and periplasm - are present. However, the excess membrane triples the surface area of the cell relative to its volume, which may be related to Gemmata's sterol biosynthesis abilities.^[6] A 2014 study using similar methods reported confirmation of the earlier enclosed compartment hypothesis.^[7]

It has recently been shown that Gemmata obscuriglobus is able to take in large molecules via a process which in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external items.^[8][9]

Genome

RNA sequencing shows that the planctomycetes are related to the Verrucomicrobia and possibly the Chlamydiae.^[10] A number of essential pathways are not organised as operons, which is unusual for bacteria.^[11] A number of genes have been found (through sequence comparisons) that are similar to genes found in eukaryotes. One such example is a gene sequence (in Gemmata obscuriglobus) that was found to have significant homology to the integrin alpha-V, a protein that is important in transmembrane signal transduction in eukaryotes.^[12]

Life cycle

The life cycle of many planctomycetes involves alternation between sessile cells and flagellated swarmer cells. The sessile cells bud to form the flagellated swarmer cells which swim for a while before settling down to attach and begin reproduction.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[13] and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project.^[14]

Phycisphaera mikrensis Fukunaga et al. 2010 Planctomycetales ?Candidatus Nostocoida limicola III Brocadiaceae Candidatus Scalindua ?Candidatus S. arabica Woebken et al. 2008 ?Candidatus S. marina Van de Vossenberg et al. 2007 ?Candidatus S. profunda Van De Vossenberg et al. 2008 ?Candidatus S. richardsii Fuchsman et al. 2012 Candidatus S. wagneri Schmid et al. 2003 Candidatus S. sorokinii Kuypers et al. 2003 Candidatus S. brodae Schmid et al. 2003 Candidatus Kuenenia stuttgartiensis Schmid et al. 2000 Candidatus Brocadia Candidatus B. anammoxidans Jetten et al. 2001 Candidatus B. brasiliensis Araujo et al. 2011 Candidatus B. caroliniensis Candidatus B. fulgida Kartal et al. 2004 Candidatus B. sinica Hu et al. 2010 Candidatus Anammoxoglobus propionicus Kartal et al. 2006 Candidatus Jettenia asiatica Quan et al. 2008 Planctomycetaceae Planctomyces ?P. bekefii ♪ Gimesi 1924 (type sp.) ?P. guttaeformis ♪ (ex Hortobágyi 1965) Starr and Schmidt 1984 ?P. stranskae ♪ (ex Wawrik 1952) Starr and Schmidt 1984 P. brasiliensis Schlesner 1990 P. maris (ex Bauld and Staley 1976) Bauld and Staley 1980 P. limnophilus Hirsch and Müller 1986 Schlesneria paludicola Kulichevskaya et al. 2007 Rhodopirellula R. baltica Schlesner et al. 2004 (type sp.) R. europaea ♠ Frank 2011 R. maiorica ♠ Frank 2011 R. sallentina ♠ Frank 2011 Blastopirellula marina (Schlesner 1987) Schlesner et al. 2004 Pirellula staleyi Schlesner and Hirsch 1987 Gemmata obscuriglobus Franzmann and Skerman 1985 Telmatocola sphagniphila Kulichevskaya et al. 2012 Zavarzinella formosa Kulichevskaya et al. 2009 Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 Aquisphaera giovannonii Bondoso et al. 2011 Singulisphaera ?S. mucilaginosa ♠ Zaicnikova et al. 2011 S. acidiphila Kulichevskaya et al. 2008 (type sp.) S. rosea Kulichevskaya et al. 2012

Notes:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)
♪ Prokaryotes where no pure (axenic) cultures are isolated or available, i. e. not cultivated or can not be sustained in culture for more than a few serial passages

References

1. Jeske, O., Schueler, M., Schumann, P., Schneider, A., Boedeker, C., Jogler, M., Bollschweiler, D., Rohde, M., Mayer, C., Engelhardt, H., Spring, S. & Jogler, C. (2015). "Planctomycetes do possess a peptidoglycan cell wall". Nature Communications 6: 7116. doi:10.1038/ncomms8116. PMID 25964217.
2. van Teeseling, M.C.F., Mesman, R.J., Kuru, E., Espaillat, A., Cava, F., Brun, Y.V., VanNieuwenhze, M.S., Kartal, B & van Niftrik, L. (2015). "Anammox Planctomycetes have a peptidoglycan cell wall". Nature Communications 6: 6878. doi:10.1038/ncomms7878.
3. Lindsay, M. R.; Webb, R. I.; Strous, M; Jetten, M. S.; Butler, M. K.; Forde, R. J.; Fuerst, J. A. (2001). "Cell compartmentalisation in planctomycetes: Novel types of structural organisation for the bacterial cell". Archives of microbiology 175 (6): 413–29. doi:10.1007/s002030100280. PMID 11491082.
4. Glöckner, F. O.; Kube, M; Bauer, M; Teeling, H; Lombardot, T; Ludwig, W; Gade, D; Beck, A; Borzym, K; Heitmann, K; Rabus, R; Schlesner, H; Amann, R; Reinhardt, R (2003). "Complete genome sequence of the marine planctomycete Pirellula sp. Strain 1". Proceedings of the National Academy of Sciences 100 (14): 8298–303. doi:10.1073/pnas.1431443100. PMC 166223. PMID 12835416.
5. Fieseler, L; Horn, M; Wagner, M; Hentschel, U (June 2004). "Discovery of the novel candidate phylum "Poribacteria" in marine sponges.". Applied and Environmental Microbiology 70 (6): 3724–32. doi:10.1128/aem.70.6.3724-3732.2004. PMC 427773. PMID 15184179.
6. Santarella-Mellwig, R., Pruggnaller, S., Roos, N., Mattaj, I., & Devos, D. (2013). "Three-Dimensional Reconstruction of Bacteria with a Complex Endomembrane System". PLoS Biology 11: e1001565. doi:10.1371/journal.pbio.1001565. PMID 23700385.
7. Sagulenko, E; Morgan, G. P.; Webb, R. I.; Yee, B; Lee, K. C.; Fuerst, J. A. (2014). "Structural studies of planctomycete Gemmata obscuriglobus support cell compartmentalisation in a bacterium". PLoS ONE 9 (3): e91344. doi:10.1371/journal.pone.0091344. PMC 3954628. PMID 24632833.
8. Lonhienne, Thierry G. A.; Sagulenko, Evgeny; Webb, Richard I.; Lee, Kuo-Chang; Franke, Josef; Devos, Damien P.; Nouwens, Amanda; Carroll, Bernard J. & Fuerst, John A. (2010). "Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus". Proceedings of the National Academy of Sciences 107 (29): 12883–12888. doi:10.1073/pnas.1001085107. PMC 2919973. PMID 20566852.
9. Williams, Caroline (2011). "Who are you calling simple?". New Scientist 211 (2821): 38–41. doi:10.1016/S0262-4079(11)61709-0
10. Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F., Feng L., Wang L., Alam M. 2008 Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol. Direct. 3(1):26.
11. F. O. Glöckner, M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K. Borzym, K. Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt (2003) Complete genome sequence of the marine planctomycete Pirellula sp. strain 1 PNAS 100:14 8298-8303 doi=10.1073/pnas.1431443100 pmid= 12835416 pmc=166223
12. Cheryl Jenkins, Vishram Kedar, and John A. Fuerst (2002) Gene discovery within the planctomycete division of the domain Bacteria Genome Biology 3:6 1-11
13. See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Planctomycetes". Retrieved 2013-03-20.
14. See the All-Species Living Tree Project . Data extracted from the "16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.

External links

• Beyond Prokaryotes and Eukaryotes : Planctomycetes and Cell Organization.
• Gemmata at Microbewiki