Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048.
Elshahed MS, Najar FZ, Aycock M, Qu C, Roe BA, Krumholz LR. Metagenomic analysis of the microbial community at Zodletone Spring (Oklahoma): insights into the genome of a member of the novel candidate division OD1. Applied and environmental microbiology. Am Soc Microbiol. 2005;71:7598–602.
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012;337:1661–5.
Mohiuddin MM, Salama Y, Schellhorn HE, Golding GB. Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens. Water Res. 2017;115:360–9.
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499:431–7.
Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, et al. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO(2) concentrations. Environ Microbiol. 2017;19:459–74.
Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CM, Emerson JB, et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat Microbiol. 2018;3:328–36.
Correa-Galeote D, Bedmar EJ, Fernández-González AJ, Fernández-López M, Arone GJ. Bacterial communities in the rhizosphere of amilaceous maize (Zea mays L.) as assessed by pyrosequencing. Front Plant Sci. 2016;7:1016.
Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol. 2016;92:fiw018. https://doi.org/10.1093/femsec/fiw018.
Wurzbacher C, Nilsson RH, Rautio M, Peura S. Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds. ISME J. 2017;11:1938–41.
Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, et al. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Front Microbiol. 2020;11:1848.
He X, McLean JS, Edlund A, Yooseph S, Hall AP, Liu S-Y, et al. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci USA. 2015;112:244–9.
Baker JL, Morton JT, Dinis M, Alvarez R, Tran NC, Knight R, et al. Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. Genome Res. 2021;31:64–74.
Shaiber A, Willis AD, Delmont TO, Roux S, Chen L-X, Schmid AC, et al. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol. 2020;21:1–35.
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 2015;523:208–11.
Danczak R, Johnston M, Kenah C, Slattery M, Wrighton KC, Wilkins M. Members of the Candidate Phyla Radiation are functionally differentiated by carbon-and nitrogen-cycling capabilities. Microbiome. 2017;5:1–14.
Herrmann M, Wegner C-E, Taubert M, Geesink P, Lehmann K, Yan L, et al. Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Front Microbiol. 2019;10:1407.
He C, Keren R, Whittaker ML, Farag IF, Doudna JA, Cate JH, et al. Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. Nat Microbiol. 2021;6:354–65.
Vigneron A, Cruaud P, Langlois V, Lovejoy C, Culley AI, Vincent WF. Ultra-small and abundant: candidate phyla radiation bacteria are potential catalysts of carbon transformation in a thermokarst lake ecosystem. Limnol Oceanogr Lett. 2020;5:212–20.
Vavourakis CD, Andrei A-S, Mehrshad M, Ghai R, Sorokin DY, Muyzer G. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome. 2018;6:1–18.
Luef B, Frischkorn KR, Wrighton KC, Holman H-YN, Birarda G, Thomas BC, et al. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun. 2015;6:1–8.
Castelle CJ, Banfield JF. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell. 2018;172:1181–97.
Gleeson T, Befus KM, Jasechko S, Luijendijk E, Cardenas MB. The global volume and distribution of modern groundwater. Nat Geosci. 2016;9:161–7.
Krüger M, Potthast K, Michalzik B, Tischer A, Küsel K, Deckner FF, et al. Drought and rewetting events enhance nitrate leaching and seepage-mediated translocation of microbes from beech forest soils. Soil Biol Biochem. 2021;154:108153.
Starr EP, Shi S, Blazewicz SJ, Probst AJ, Herman DJ, Firestone MK, et al. Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. Microbiome. 2018;6:1–12.
Nicolas AM, Jaffe AL, Nuccio EE, Taga ME, Firestone MK, Banfield JF. Soil Candidate Phyla Radiation bacteria encode components of aerobic metabolism and co-occur with nanoarchaea in the rare biosphere of rhizosphere grassland communities. Msystems. 2021;6:e01205-e1220.
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533–8.
Gong J, Qing Y, Guo X, Warren A. “Candidatus Sonnebornia yantaiensis”, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea). Syst Appl Microbiol. 2014;37:35–41.
Bor B, Collins A, Murugkar P, Balasubramanian S, To T, Hendrickson E, et al. Insights obtained by culturing Saccharibacteria with their bacterial hosts. J Dent Res. 2020;99:685–94.
Cross KL, Campbell JH, Balachandran M, Campbell AG, Cooper SJ, Griffen A, et al. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nat Biotechnol. 2019;37:1314–21.
Murugkar PP, Collins AJ, Chen T, Dewhirst FE. Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts. J Oral Microbiol. 2020;12:1814666.
Utter DR, He X, Cavanaugh CM, McLean JS, Bor B. The saccharibacterium TM7x elicits differential responses across its host range. ISME J. 2020;14:3054–67.
Moreira D, Zivanovic Y, López-Archilla AI, Iniesto M, López-García P. Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii. Nat Commun. 2021;12:1–11.
Giovannoni SJ, Thrash JC, Temperton B. Implications of streamlining theory for microbial ecology. ISME J. 2014;8:1553–65.
Dufresne A, Garczarek L, Partensky F. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 2005;6:1–10.
Küsel K, Totsche KU, Trumbore SE, Lehmann R, Steinhäuser C, Herrmann M. How deep can surface signals be traced in the critical zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape. Front Earth Sci. 2016;4:32.
Yan L, Herrmann M, Kampe B, Lehmann R, Totsche KU, Küsel K. Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Res. 2020;170:115341.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–6.
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nature Microbiol. 2021;6:3–6.
Campbell JH, O’Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, et al. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci. 2013;110:5540–5.
Kersey CM, Agyemang PA, Dumenyo CK. CorA, the magnesium/nickel/cobalt transporter, affects virulence and extracellular enzyme production in the soft rot pathogen Pectobacterium carotovorum. Mol Plant Pathol. 2012;13:58–71.
Porcheron G, Garénaux A, Proulx J, Sabri M, Dozois CM. Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence. Front Cell Infect Microbiol. 2013;3:90.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Yan L, Hermans SM, Totsche KU, Lehmann R, Herrmann M, Küsel K. Groundwater bacterial communities evolve over time in response to recharge. Water Res. 2021;201:117290.
Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, et al. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. 2020;8:1–15.
Castelle CJ, Brown CT, Thomas BC, Williams KH, Banfield JF. Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. Sci Rep. 2017;7:1–12.
Kohlhepp B, Lehmann R, Seeber P, Küsel K, Trumbore SE, Totsche KU. Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate–siliciclastic alternations of the Hainich CZE, central Germany. Hydrol Earth Syst Sci. 2017;21:6091–116.
Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol. 2014;90:39–53.
Wegner C-E, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K, et al. Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of the elements nitrogen, sulfur, and carbon. Appl Environ Microbiol. 2019;85:e02346-e2418.
Ozawa K, Meikari T, Motohashi K, Yoshida M, Akutsu H. Evidence for the presence of an F-type ATP synthase involved in sulfate respiration in Desulfovibrio vulgaris. J Bacteriol. 2000;182:2200–6.
Nelson WC, Stegen JC. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Front Microbiol. 2015;6:713.
McLean JS, Bor B, Kerns KA, Liu Q, To TT, Solden L, et al. Acquisition and adaptation of ultra-small parasitic reduced genome bacteria to mammalian hosts. Cell Rep. 2020;32:107939.
Batinovic S, Rose JJ, Ratcliffe J, Seviour RJ, Petrovski S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nat Microbiol. 2021;6:703–11.
Levin PA, Angert ER. Small but mighty: cell size and bacteria. Cold Spring Harb Perspect Biol. 2015;7:a019216.
Kempes CP, Wang L, Amend JP, Doyle J, Hoehler T. Evolutionary tradeoffs in cellular composition across diverse bacteria. ISME J. 2016;10:2145–57.
Melville S, Craig L. Type IV pili in Gram-positive bacteria. Microbiol Mol Biol Rev. 2013;77:323–41.
Craig L, Volkmann N, Arvai AS, Pique ME, Yeager M, Egelman EH, et al. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell. 2006;23:651–62.
Mandlik A, Swierczynski A, Das A, Ton-That H. Pili in Gram-positive bacteria: assembly, involvement in colonization and biofilm development. Trends Microbiol. 2008;16:33–40.
Xie B, Wang J, Nie Y, Chen D, Hu B, Wu X, et al. EpicPCR-directed cultivation of a candidatus saccharibacteria symbiont reveals a type IV Pili-dependent epibiotic lifestyle. bioRxiv. https://www.biorxiv.org/content/early/2021/07/08/2021.07.08.451036.
Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, et al. A rooted phylogeny resolves early bacterial evolution. Science. 2021;372:eabe0511.
Lehmann K, Lehmann R, Totsche KU. Event-driven dynamics of the total mobile inventory in undisturbed soil account for significant fluxes of particulate organic carbon. Sci Total Environ. 2021;756:143774.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Ultsch A, Mörchen F. ESOM-Maps: tools for clustering, visualization, and classification with Emergent SOM. DATA BIONICS RESEARCH GROUP: UNIVERSITY OF MARBURG; 2005.
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 2009;10:1–16.
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.
Gruber-Vodicka HR, Seah BK, Pruesse E. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. Msystems. 2020;5:e00920-e1020.
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Oxford University Press; 2020.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:1–11.
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 2020;48:8883–900.
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353–61.
Rawlings ND, Barrett AJ, Bateman A. MEROPS: the peptidase database. Nucleic Acids Res. 2010;38:D227–33.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47:D427–32.
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95-101.
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
Emiola A, Oh J. High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage. Nat Commun. 2018;9:1–8.
R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing; 2020. https://www.R-project.org/.
Quinn TP, Richardson MF, Lovell D, Crowley TM. propr: an R-package for identifying proportionally abundant features using compositional data analysis. Sci Rep. 2017;7:1–9.
Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal Complex Syst. 2006;1695:1–9.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. RCy3: network biology using Cytoscape from within R. F1000Research. 2019;8:1774.
Kassambara A. rstatix: pipe-friendly framework for basic statistical tests. 2020. https://CRAN.R-project.org/package=rstatix.