Cuniculiplasmataceae, their ecogenomic and metabolic patterns, and interactions with ‘ARMAN’
Tóm tắt
Recently, the order Thermoplasmatales was expanded through the cultivation and description of species Cuniculiplasma divulgatum and corresponding family Cuniculiplasmataceae. Initially isolated from acidic streamers, signatures of these archaea were ubiquitously found in various low-pH settings. Eight genomes with various levels of completeness are currently available, all of which exhibit very high sequence identities and genomic conservation. Co-existence of Cuniculiplasmataceae with archaeal Richmond Mine acidophilic nanoorganisms (‘ARMAN’)-related archaea representing an intriguing group within the “microbial dark matter” suggests their common fundamental environmental strategy and metabolic networking. The specific case of “Candidatus Mancarchaeum acidiphilum” Mia14 phylogenetically affiliated with “Ca. Micrarchaeota” from the superphylum “Ca. Diapherotrites” along with the presence of other representatives of ‘DPANN’ with significantly reduced genomes points at a high probability of close interactions between the latter and various Thermoplasmatales abundant in situ. This review critically assesses our knowledge on specific functional role and potential of the members of Cuniculiplasmataceae abundant in acidophilic microbiomes through the analysis of distribution, physiological and genomic patterns, and their interactions with ‘ARMAN’-related archaea.
Tài liệu tham khảo
Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320(5879):1047–1050
Baker BJ, Banfield JF (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44:139–152
Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science 314(5807):1933–1935
Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF (2010) Enigmatic, ultrasmall, uncultivated archaea. Proc Natl Acad Sci USA 107(19):8806–8811
Chen LX, Méndez-García C, Dombrowski N, Servín-Garcidueñas LE, Eloe-Fadrosh EA, Fang BZ, Luo ZH, Tan S, Zhi XY, Hua ZS, Martinez-Romero E, Woyke T, Huang LN, Sánchez J, Peláez AI, Ferrer M, Baker BJ, Shu WS (2018) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J 12(3):756–775
Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J 3:159–167
Darland G, Brock TD, Samsonoff W, Conti SF (1970) A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 170(3965):1416–1418
Fütterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G, Liebl W (2004) Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci USA 101(24):9091–9096
Golyshina OV (2011) Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae. Appl Environ Microbiol 77:5071–5078
Golyshina OV (2014) The family ferroplasmaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes: other major lineages of bacteria and the archaea. Springer Verlag, Berlin Heidelberg, pp 29–34
Golyshina OV, Pivovarova TA, Karavaiko GI, Kondratéva TF, Moore ER, Abraham WR, Lünsdorf H, Timmis KN, Yakimov MM, Golyshin PN (2000) Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the archaea. Int J Syst Evol Microbiol 50(3):997–1006
Golyshina OV, Lünsdorf H, Kublanov IV, Goldenstein NI, Hinrichs KU, Golyshin PN (2016a) The novel, extremely acidophilic, cell wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family of Cuniculiplasmataceae fam. nov., order Thermoplasmatales. Int J Syst Evol Microbiol 66:332–340
Golyshina OV, Kublanov IV, Tran H, Korzhenkov AA, Lünsdorf H, Nechitaylo TY, Gavrilov SN, Toshchakov SV, Golyshin PN (2016b) Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments. Sci Rep 6:39034
Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN (2017a) Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y(T). Sci Rep 7(1):3682
Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN (2017b) “ARMAN” archaea depend on association with euryarchaeal host in culture and in situ. Nat Commun 8:60
Jones DS, Albrecht HL, Dawson KS, Schaperdoth I, Freeman KH, Pi Y, Pearson A, Macalady JL (2012) Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME J 6:158–170
Justice NB, Pan C, Mueller R, Spaulding SE, Shah V, Sun CL, Yelton AP, Miller CS, Thomas BC, Shah M, VerBerkmoes N, Hettich R, Banfield JF (2012) Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl Environ Microbiol 78:8321–8330
Kato S, Itoh T, Yamagishi A (2011) Archaeal diversity in a terrestrial acidic spring field revealed by a novel PCR primer targeting archaeal 16S rRNA genes. FEMS Microbiol Lett 319(1):34–43
Krause S, Bremges A, Münch PC, McHardy AC, Gescher J (2017) Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms. Sci Rep 7(1):3289
Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV (2018) Viruses of archaea: structural, functional, environmental and evolutionary genomics. Virus Res 244:181–193
Méndez-García C, Mesa V, Sprenger RR, Richter M, Diez MS, Solano J, Bargiela R, Golyshina OV, Manteca Á, Ramos JL, Gallego JR, Llorente I, Martins dos Santos VA, Jensen ON, Peláez AI, Sánchez J, Ferrer M (2014) Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage. ISME J 8(6):1259–1274
Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M (2015) Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 6:475
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978):37–43
Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434(7036):1011–1014
Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF (2013) Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genom 14:485
Ziegler S, Dolch K, Geiger K, Krause S, Asskamp M, Eusterhues K, Kriews M, Wilhelms-Dick D, Goettlicher J, Majzlan J, Gescher J (2013) Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. ISME J 7(9):1725–1737