Candidate division TM7

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The candidate division TM7, is a major lineage of Bacteria, the existence of which is known solely through environmental 16S rRNA sequences as to date no species has been grown in the lab, a requirement for taxonomy, making it a candidate phylum.[1] Along with Candidate divisions TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog from near Gifhorn, Lower Saxony, Germany(52°30′N 10°30′E / 52.500°N 10.500°E / 52.500; 10.500), where 262 PCR amplified 16S rDNA fragments were cloned into a plasmid vector, named TM clones for 'Torf, Mittlere Schicht' (= peat, middle layer),.[2] It has been found in several environments since such as from activated sludges,[3][4] water-treatment plant sludge[5] rainforest soil,[6] human salive,[7][8] in association with sponges,[9] cockroaches,[10] gold mines[11] and other environments (bar thermophilic), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a,[12] suggesting metabolically active TM7 in environmental sites may serve as model organisms to better understand the role TM7 play in human health.

Properties[edit]


Chloroflexi






ABY1



BD1-5 group





OP11



WS6






TM7




SC3




WS5



Guaymas1






Relationship of phylum TM7 and its closest relatives, including the Chloroflexi[13]

Species singled out with TM7 specific FISH probes form a bioreactor sludge revealed the presence of a gram-positive cell envelopes and several morphotypes: a sheathed filament (abundant), a rod occurring in short chains, a thick filament and cocci; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges).[5] The majority of bacterial phyla are Gram-negative diderms, whereas only the Firmicutes, the Actinobacteria and Chloroflexi are monoderms. Candidate phylum TM7 is in fact a close relative of the Chloroflexi.[13]

Using a polycarbonate membrane as a growth support and soil extract as the substrate, microcolonies of this clade were grown consisting of long filamentous rods up to 15 μm long with less than 50 cells or short rods with several hundred cells per colony, after 10 days incubation.[14]

Thanks to a microfluidic chip allowing the isolation and amplification of the genome of a single cell, the genome of 3 long filament morphology cells with identical 16S rRNA were sequenced to create a draft sequence of the genome confirming some previously ascertained properties, elucidating some of its metabolic capabilities, revealing novel genes and hinting to potential pathogenic abilities.[15]

Over 50 different phylotypes have been identified[13] and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%.[5] An interactive phylogenetic tree of TM7,[12] built using jsPhyloSVG,[16] allows for quick access to GenBank sequences and distance matrix calculations between tree branches.

Stable isotope probing studies have found that some members of this phylum can degrade toluene.[17][18]

TM7 Candidate Division neighbor-joining phylogenetic tree

References[edit]

  1. ^ Pace, N. R. (2009). "Mapping the Tree of Life: Progress and Prospects". Microbiology and Molecular Biology Reviews 73 (4): 565–576. doi:10.1128/MMBR.00033-09. PMC 2786576. PMID 19946133.  edit
  2. ^ Rheims, H.; Rainey, F. A.; Stackebrandt, E. (1996). "A molecular approach to search for diversity among bacteria in the environment". Journal of Industrial Microbiology & Biotechnology 17 (3–4): 159. doi:10.1007/BF01574689.  edit
  3. ^ Bond, PL; Hugenholtz, P; Keller, J; Blackall, LL (1995). "Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors". Applied and environmental microbiology 61 (5): 1910–6. PMC 167453. PMID 7544094.  edit
  4. ^ Godon, JJ; Zumstein, E; Dabert, P; Habouzit, F; Moletta, R (1997). "Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis". Applied and environmental microbiology 63 (7): 2802–13. PMC 168577. PMID 9212428.  edit
  5. ^ a b c Hugenholtz, P.; Tyson, G. W.; Webb, R. I.; Wagner, A. M.; Blackall, L. L. (2001). "Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives". Applied and Environmental Microbiology 67 (1): 411–419. doi:10.1128/AEM.67.1.411-419.2001. PMC 92593. PMID 11133473.  edit
  6. ^ Borneman, J; Triplett, EW (1997). "Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation". Applied and environmental microbiology 63 (7): 2647–53. PMC 168563. PMID 9212415.  edit
  7. ^ Lazarevic, V.; Whiteson, K.; Hernandez, D.; Francois, P.; Schrenzel, J. (2010). "Study of inter- and intra-individual variations in the salivary microbiota". BMC Genomics 11: 523. doi:10.1186/1471-2164-11-523. PMC 2997015. PMID 20920195.  edit
  8. ^ Dewhirst, F. E.; Chen, T.; Izard, J.; Paster, B. J.; Tanner, A. C. R.; Yu, W. -H.; Lakshmanan, A.; Wade, W. G. (2010). "The Human Oral Microbiome". Journal of Bacteriology 192 (19): 5002–5017. doi:10.1128/JB.00542-10. PMC 2944498. PMID 20656903.  edit
  9. ^ Thiel, V.; Leininger, S.; Schmaljohann, R.; Brümmer, F.; Imhoff, J. F. (2007). "Sponge-specific Bacterial Associations of the Mediterranean Sponge Chondrilla nucula (Demospongiae, Tetractinomorpha)". Microbial Ecology 54 (1): 101–111. doi:10.1007/s00248-006-9177-y. PMID 17364249.  edit
  10. ^ Berlanga, M; Paster, BJ; Guerrero, R (2009). "The taxophysiological paradox: changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host". International microbiology : the official journal of the Spanish Society for Microbiology 12 (4): 227–36. PMID 20112227.  edit
  11. ^ Rastogi, G.; Stetler, L. D.; Peyton, B. M.; Sani, R. K. (2009). "Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA". The Journal of Microbiology 47 (4): 371–384. doi:10.1007/s12275-008-0249-1. PMID 19763410.  edit
  12. ^ a b Dinis, J. M.; Barton, D. E.; Ghadiri, J.; Surendar, D.; Reddy, K.; Velasquez, F.; Chaffee, C. L.; Lee, M. C. W.; Gavrilova, H.; Ozuna, H.; Smits, S. A.; Ouverney, C. C. (2011). "In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment". In Yang, Ching-Hong. PLoS ONE 6 (6): e21280. doi:10.1371/journal.pone.0021280. PMC 3118805. PMID 21701585.  edit
  13. ^ a b c Rappe, M. S.; Giovannoni, S. J. (2003). "The Uncultured Microbial Majority". Annual Review of Microbiology 57: 369–394. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284.  edit
  14. ^ Ferrari, B. C.; Binnerup, S. J.; Gillings, M. (2005). "Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria". Applied and Environmental Microbiology 71 (12): 8714–8720. doi:10.1128/AEM.71.12.8714-8720.2005. PMC 1317317. PMID 16332866.  edit
  15. ^ Marcy, Y.; Ouverney, C.; Bik, E. M.; Losekann, T.; Ivanova, N.; Martin, H. G.; Szeto, E.; Platt, D.; Hugenholtz, P.; Relman, D. A.; Quake, S. R. (2007). "Inaugural Article: Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth". Proceedings of the National Academy of Sciences 104 (29): 11889. Bibcode:2007PNAS..10411889M. doi:10.1073/pnas.0704662104.  edit
  16. ^ Smits, S. A.; Ouverney, C. C. (2010). "JsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web". In Poon, Art F. Y. PLoS ONE 5 (8): e12267. doi:10.1371/journal.pone.0012267. PMC 2923619. PMID 20805892.  edit
  17. ^ Xie, S.; Sun, W.; Luo, C.; Cupples, A. M. (2010). "Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing". Biodegradation 22 (1): 71–81. doi:10.1007/s10532-010-9377-5. PMID 20549308.  edit
  18. ^ Luo, C.; Xie, S.; Sun, W.; Li, X.; Cupples, A. M. (2009). "Identification of a Novel Toluene-Degrading Bacterium from the Candidate Phylum TM7, as Determined by DNA Stable Isotope Probing". Applied and Environmental Microbiology 75 (13): 4644–4647. doi:10.1128/AEM.00283-09. PMC 2704817. PMID 19447956.  edit