Patescibacteria Superphylum
Patescibacteria is a large group of bacteria prevalent in aquifer environments like groundwater. The superphylum Patescibacteria was first proposed by Rinke et al. in 2013[1] to include OD1 (Parcubacteria), OP11 (Microgenomates), and GN02 (Gracilibacteria). Brown et al. then extended the Parcubacteria and Microgenomates to superphyla with 26 candidate phyla by recovering metagenome-assembled genomes (MAGs) from groundwater samples in 2015. A concept, candidate phylum radiation (CPR), was used to describe these newly defined phyla for the first time.[2] In 2016, Anantharaman et al. proposed 47 candidate phyla from groundwater and sediment samples, and some of these were affiliated with Patescibacteria.[3]
Some common features of Patescibacteria include their ultra-small cell size (e.g. 0.3 micron), reduced genome size (~1 Mbp) and lack of bacterial immune system against phage, CRISPR.[2][4]
Patescibacteria is abundant in aquifer environments, especially in groundwater.[2][5][6] Tian et al.[7] and Herrmann et al.[8] proposed the adaptive mechanisms of Patescibacteria for its prevalence in groundwater environments. Now much attention has been paid to the superphylum for its impact on the view of the tree of life and microbial diversity.[9][10][11][12]
The nomenclature Patescibacteria (phylum level) has been admitted in SILVA and GTDB databases. Sometimes Patescibacteria is also referred to as CPR, which is a general name rather than a nomenclature to describe a group of newly discovered phyla covering Patescibacteria and more.
References
- ↑ Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; et al. (July 18, 2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. PMID 23851394. Unknown parameter
|s2cid=ignored (help) - ↑ 2.0 2.1 2.2 Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.; et al. (July 18, 2015). "Unusual biology across a group comprising more than 15% of domain Bacteria". Nature. 523 (7559): 208–211. Bibcode:2015Natur.523..208B. doi:10.1038/nature14486. OSTI 1512215. PMID 26083755. Unknown parameter
|s2cid=ignored (help) - ↑ Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; et al. (October 24, 2016). "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system". Nature Communications. 7 (1): 13219. Bibcode:2016NatCo...713219A. doi:10.1038/ncomms13219. PMC 5079060. PMID 27774985.
- ↑ Burstein, David; Sun, Christine L.; Brown, Christopher T.; et al. (February 3, 2016). "Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems". Nature Communications. 7 (1): 10613. Bibcode:2016NatCo...710613B. doi:10.1038/ncomms10613. PMC 4742961. PMID 26837824.
- ↑ Luef, Birgit; Frischkorn, Kyle R.; Wrighton, Kelly C.; et al. (February 27, 2015). "Diverse uncultivated ultra-small bacterial cells in groundwater". Nature Communications. 6 (1): 6372. Bibcode:2015NatCo...6.6372L. doi:10.1038/ncomms7372. PMID 25721682.
- ↑ Proctor, Caitlin R.; Besmer, Michael D.; Langenegger, Timon; et al. (May 18, 2018). "Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems". The ISME Journal. 12 (5): 1344–1359. doi:10.1038/s41396-018-0070-8. PMC 5932017. PMID 29416124.
- ↑ Tian, Renmao; Ning, Daliang; He, Zhili; et al. (April 6, 2020). "Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity". Microbiome. 8 (1): 51. doi:10.1186/s40168-020-00825-w. PMC 7137472 Check
|pmc=value (help). PMID 32252814 Check|pmid=value (help). - ↑ Herrmann, Martina; Wegner, Carl-Eric; Taubert, Martin; Geesink, Patricia; Lehmann, Katharina; Yan, Lijuan; Lehmann, Robert; Totsche, Kai Uwe; Küsel, Kirsten (2019). "Predominance of Cand. Patescibacteria in Groundwater is Caused by Their Preferential Mobilization from Soils and Flourishing Under Oligotrophic Conditions". Frontiers in Microbiology. 10: 1407. doi:10.3389/fmicb.2019.01407. PMC 6596338 Check
|pmc=value (help). PMID 31281301. - ↑ Castelle, Cindy J.; Banfield, Jillian F. (March 8, 2018). "Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life". Cell. 172 (6): 1181–1197. doi:10.1016/j.cell.2018.02.016. PMID 29522741 – via PubMed. Unknown parameter
|s2cid=ignored (help) - ↑ Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; et al. (April 11, 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647. Unknown parameter
|s2cid=ignored (help) - ↑ Castelle, Cindy J.; Brown, Christopher T.; Anantharaman, Karthik; et al. (October 18, 2018). "Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations". Nature Reviews Microbiology. 16 (10): 629–645. doi:10.1038/s41579-018-0076-2. PMID 30181663. Unknown parameter
|s2cid=ignored (help) - ↑ Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.; et al. (March 18, 2018). "Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface". Nature Microbiology. 3 (3): 328–336. doi:10.1038/s41564-017-0098-y. PMC 6792436 Check
|pmc=value (help). PMID 29379208.
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